<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"><style>body { line-height: 1.5; }blockquote { margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em; }body { font-size: 10.5pt; font-family: 微软雅黑; color: rgb(0, 0, 0); line-height: 1.5; }</style></head><body>
<div><span></span></div><div><span><div style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt">From my understanding, the origin should <span style="font-size: 13.3333px; background-color: transparent;">not </span><span style="font-size: 10pt; line-height: 1.5; background-color: transparent;">be a problem. </span></div><div style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt"><span style="font-size: 10pt; line-height: 1.5; background-color: transparent;">For standard Cu2O with space group of pn-3m, the atomic sites for both Cu and O should be well set already. However, the euivalent sites for both oxygen/or Cu should be carefully considered if you shift the orign of the molecules. </span></div><div style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt">origin 1 Cu 4b（0.25 0.25 0.25） and O 2a (0 0 0)</div></span></div>
<blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><div> </div><img src="cid:_Foxmail.1@8f8d5ab2-bac3-d643-a4f7-67aca313bada" border="0"></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em">origin 2 Cu 4c (0.5 0.5 0.5) and O 2a （0.25 0.25 0.25）</blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><br></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><img src="cid:_Foxmail.1@920a61b9-2fed-ff76-6b27-d1e05a02d2d2" border="0"></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><br></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><br></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em">the previous 4b sites changed to 4c, instead. </blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><br></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em">Correct me if I am wrong. </blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><br></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em">Best regards,</blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em">Wen Wen </blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><br></blockquote><blockquote style="margin-Top: 0px; margin-Bottom: 0px; margin-Left: 0.5em"><br><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"><div style="PADDING-RIGHT: 8px; PADDING-LEFT: 8px; FONT-SIZE: 12px;FONT-FAMILY:tahoma;COLOR:#000000; BACKGROUND: #efefef; PADDING-BOTTOM: 8px; PADDING-TOP: 8px"><div><b>From:</b> <a href="mailto:gsas-ii-request@aps.anl.gov">gsas-ii-request</a></div><div><b>Date:</b> 2019-08-23 01:00</div><div><b>To:</b> <a href="mailto:gsas-ii@aps.anl.gov">gsas-ii</a></div><div><b>Subject:</b> GSAS-II Digest, Vol 230, Issue 1</div></div></div><div><div>Send GSAS-II mailing list submissions to</div>
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<div>Today's Topics:</div>
<div> </div>
<div> 1. Problem with intensities (my previous email) (Ivo Alxneit)</div>
<div> 2. Re: Problem with intensities (my previous email)</div>
<div> (Leopoldo Suescun)</div>
<div> </div>
<div> </div>
<div>----------------------------------------------------------------------</div>
<div> </div>
<div>Message: 1</div>
<div>Date: Thu, 22 Aug 2019 14:36:33 +0200</div>
<div>From: Ivo Alxneit <ivo.alxneit@psi.ch></div>
<div>To: <gsas-ii@aps.anl.gov></div>
<div>Subject: [GSAS-II] Problem with intensities (my previous email)</div>
<div>Message-ID: <401d34a7-6ec6-3dd3-a275-3eb467ca0634@psi.ch></div>
<div>Content-Type: text/plain; charset="utf-8"</div>
<div> </div>
<div>Dear all</div>
<div> </div>
<div>I could resolve my problem by selecting the other possible origin</div>
<div>(translated by (1/4, 1/4, 1/4) for Cu2O. But (being not really a</div>
<div>crystallographer) this confuses me a bit. In my understanding, origin 1</div>
<div>or 2 give just two alternate description of the same structure. It may</div>
<div>be more or less convenient to choose one or the other because both</div>
<div>describe the identical structure. Intensities on the other hand are real</div>
<div>physical properties. Why are they affected by the (free) choice of the</div>
<div>origin? Also, VESTA gives me the opposite pattern than GSASII for the</div>
<div>two different choices of the origin i.e. I get differing pattern for</div>
<div>both choices of the origin.</div>
<div> </div>
<div>thanks for any clarification</div>
<div>-- </div>
<div>Dr. Ivo Alxneit</div>
<div>Catalysis for Energy Group</div>
<div>Bioenergy and Catalysis Laboratory phone: +41 56 310 4092</div>
<div>Paul Scherrer Institute fax: +41 56 310 2688</div>
<div>CH-5232 Villigen gnupg key: 0x515E30C7</div>
<div>Switzerland</div>
<div>https://www.psi.ch/ceg/</div>
<div> </div>
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<div>Message: 2</div>
<div>Date: Thu, 22 Aug 2019 10:30:08 -0300</div>
<div>From: Leopoldo Suescun <leopoldo@fq.edu.uy></div>
<div>To: Ivo Alxneit <ivo.alxneit@psi.ch></div>
<div>Cc: gsas-ii@aps.anl.gov</div>
<div>Subject: Re: [GSAS-II] Problem with intensities (my previous email)</div>
<div>Message-ID:</div>
<div> <CAAeV=tjzG8js0795LeDF=Js8KpDyND1zkPncniVarwaM-HC__g@mail.gmail.com></div>
<div>Content-Type: text/plain; charset="utf-8"</div>
<div> </div>
<div>Dear Ivo,</div>
<div>Since intensities are a physical property, they do not depend on the</div>
<div>arbitrary selection of the origin of the unit cell used to calculate it. In</div>
<div>fact, there is no origin in a crystal, just interatomic vectors.</div>
<div>When the calculation of intensity is done based on the structure factor,</div>
<div>you need to define an origin in order to compute the calculated intensity.</div>
<div>If you define the origin, all atoms automatically have fixed coordinates</div>
<div>x,y,z. So when you use a set of coordinates to describe a structure they</div>
<div>must correspond to the same origin choice. It is possible to calculate the</div>
<div>intensities independently of the origin, but it is impossible to represent</div>
<div>a stucture using a computer algorithm without using an origin.</div>
<div> </div>
<div>Since the origin choice is and will always be arbitrary (it is not a</div>
<div>physical property) you will need to use the right equations to compute your</div>
<div>structure/diffraction pattern respect to that arbitrary point. Usually the</div>
<div>point of maximum symmetry of the cell is selected as the origin (it is</div>
<div>called Origin Choice 1 in the International Tables of Crystallography Vol</div>
<div>A.). This may not be at all determined, for instance in many space groups</div>
<div>(P1, P21, Pc,P212121, etc) all points in the unit cell have the same</div>
<div>symmetry, the identity (or no symmetry at all). The origin choice,</div>
<div>therefore, is always a matter of convention and each piece of software is</div>
<div>written to handle structures expressed in some origin choice.</div>
<div> </div>
<div>Most pieces of software choose the origin at a center of symmetry since</div>
<div>this simplifies calculations (usually called Origin Choice 2 also in the</div>
<div>ITA, where both origin choices are given), but this may not be the point of</div>
<div>maximum symmetry of the unit cell, therefore, the coordinates you get from</div>
<div>a cif file or a database may not refer to the same origin choice used by</div>
<div>the software.</div>
<div> </div>
<div>When you want to represent (or do calculations with) a structure that is</div>
<div>described in one origin but the program assumes the origin is at a</div>
<div>different position you will have the wrong equations in place for the</div>
<div>structure and the result will have no physical sense.</div>
<div> </div>
<div>There are only a few space groups where this happens, you have to be</div>
<div>vigilant in those cases.</div>
<div>I hope this helps,</div>
<div>Leo</div>
<div> </div>
<div>El jue., 22 ago. 2019 a las 9:36, Ivo Alxneit via GSAS-II (<</div>
<div>gsas-ii@aps.anl.gov>) escribi?:</div>
<div> </div>
<div>> Dear all</div>
<div>></div>
<div>> I could resolve my problem by selecting the other possible origin</div>
<div>> (translated by (1/4, 1/4, 1/4) for Cu2O. But (being not really a</div>
<div>> crystallographer) this confuses me a bit. In my understanding, origin 1</div>
<div>> or 2 give just two alternate description of the same structure. It may</div>
<div>> be more or less convenient to choose one or the other because both</div>
<div>> describe the identical structure. Intensities on the other hand are real</div>
<div>> physical properties. Why are they affected by the (free) choice of the</div>
<div>> origin? Also, VESTA gives me the opposite pattern than GSASII for the</div>
<div>> two different choices of the origin i.e. I get differing pattern for</div>
<div>> both choices of the origin.</div>
<div>></div>
<div>> thanks for any clarification</div>
<div>> --</div>
<div>> Dr. Ivo Alxneit</div>
<div>> Catalysis for Energy Group</div>
<div>> Bioenergy and Catalysis Laboratory phone: +41 56 310 4092</div>
<div>> Paul Scherrer Institute fax: +41 56 310 2688</div>
<div>> CH-5232 Villigen gnupg key: 0x515E30C7</div>
<div>> Switzerland</div>
<div>> https://www.psi.ch/ceg/</div>
<div>></div>
<div>> _______________________________________________</div>
<div>> GSAS-II mailing list</div>
<div>> GSAS-II@aps.anl.gov</div>
<div>> https://mailman.aps.anl.gov/mailman/listinfo/gsas-ii</div>
<div> </div>
<div> </div>
<div> </div>
<div>-- </div>
<div>Prof. Agr. Dr. Leopoldo Suescun</div>
<div>Cryssmat-Lab/DETEMA, Facultad de Qu?mica, Universidad de la Rep?blica.</div>
<div>e-mail: leopoldo@fq.edu.uy</div>
<div>Tel: (+598) 29290705</div>
<div>Fax: (+598) 29241906*</div>
<div>Mailing address:</div>
<div>Cryssmat-Lab./DETEMA</div>
<div>Facultad de Quimica</div>
<div>Av. Gral. Flores 2124</div>
<div>Montevideo 11800</div>
<div>Uruguay</div>
<div> </div>
<div>Seguime en/Follow me at ResearchGate</div>
<div>https://www.researchgate.net/profile/Leopoldo_Suescun</div>
<div> </div>
<div>ORC*ID*: https://orcid.org/0000-0002-7606-8074</div>
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