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| 3 | <title>Use of the GSAS2CIF program</title> |
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| 4 | <meta name="keywords" content="crystallography, Rietveld, diffraction, |
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| 22 | <BLOCKQUOTE> |
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| 24 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 25 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 26 | </TH><TH><A Href="excledt.html">Previous page</A> |
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| 27 | </TH></TR></TABLE><BR CLEAR=ALL> |
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| 28 | |
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| [610] | 29 | <img src="http://www.gsas.org/Articles/gsas-logo.gif" alt="Greater Seattle Aquarium Society Logo (www.gsas.org). Used with permission" HEIGHT=80 WIDTH=150 ALIGN=RIGHT> |
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| [608] | 30 | <center><h1> |
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| 31 | <HR noshade width="75%" size="2" align="center"> |
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| 32 | Using the GSAS2CIF program |
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| 33 | <BR> |
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| 34 | to export |
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| 35 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html"> |
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| 36 | GSAS</A> |
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| 37 | results |
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| 38 | <HR noshade width="75%" size="2" align="center"> |
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| 39 | </h1></center> |
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| 40 | |
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| 41 | <P> |
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| 42 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.iucr.org/iucr-top/cif/"> |
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| 43 | The crystallographic information file, |
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| 44 | (CIF</A>) was developed by the |
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| 45 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.iucr.org"> |
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| 46 | IUCr</A> in the early 1990's |
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| 47 | as a standardized format to document single-crystal |
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| 48 | structure determinations and to exchange the results between laboratories. |
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| 49 | In the late 1990's, the |
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| 50 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.iucr.org/iucr-top/cif/pd/"> |
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| 51 | pdCIF</A> dictionary was developed to allow CIF to |
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| 52 | document powder diffraction measurements, as well as Rietveld results. |
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| 53 | A very short introduction to CIF is included at the |
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| 54 | <a href="#CIFintro">end of this document.</a> |
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| 55 | <P> |
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| 56 | The GSAS2CIF program is used to create CIFs from GSAS results. |
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| 57 | This web page documents concepts within the program as well as how the program |
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| 58 | is used. |
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| 59 | <P> |
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| 60 | <H4>Overview of the steps to create a CIF in GSAS</H4> |
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| 61 | <BLOCKQUOTE> |
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| 62 | <OL> |
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| 63 | <LI>Complete (<I>ha!</I>) your refinement, being sure to run GENLES after |
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| 64 | making any changes to the .EXP file with EXPEDT/EXPGUI. |
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| 65 | <LI>Run DISAGL to compute interatomic distances and angles. |
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| 66 | <LI>(Optional) Edit the "<a href="#pubflag"> |
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| 67 | publication flags</a>" in the distance and angle listings. |
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| 68 | <LI>(Optional) Use EXPGUI program |
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| 69 | <a href="#filltemplate">FillTemplate</A> |
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| 70 | to customize copies of CIF template files in the current directory, or |
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| 71 | manually copy these files to the current directory |
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| 72 | and use a text editor. |
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| 73 | <LI>Run GSAS2CIF (this creates experiment-specific |
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| 74 | copies of the template files). |
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| 75 | <LI>Edit the template files (for example, using |
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| 76 | <a href="#filltemplate">FillTemplate</A>) to include information. |
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| 77 | <LI>Run GSAS2CIF again, to incorporate the revised versions of the |
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| 78 | template files into the complete .CIF file. |
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| 79 | <P>... <I>and if you are like me</I>...<P> |
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| 80 | <LI>try out a few more ideas in GENLES. |
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| 81 | <LI>Run DISAGL. |
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| 82 | <LI>Run GSAS2CIF<P>... <I>repeat steps 8-10 until really finished</I>... |
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| 83 | (<a href="#ps">see quote</a>). |
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| 84 | </OL> |
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| 85 | </BLOCKQUOTE> |
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| 86 | <H4>Structure of the GSAS2CIF program</H4> |
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| 87 | <BLOCKQUOTE> |
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| 88 | <P> |
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| 89 | |
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| 90 | The GSAS2CIF program is used to prepare CIF files containing results |
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| 91 | from GSAS. It should be noted many important types of information that |
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| 92 | are needed to describe the sample and the measurement are not |
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| 93 | supplied as input to GSAS. A few examples of information that |
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| 94 | should likely be included in a CIF, but are not defined within GSAS are: |
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| [610] | 95 | the data measurement temperature, sample preparation conditions, |
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| [608] | 96 | publication information, and so on. |
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| [610] | 97 | If the CIF will be used as supplementary material, to accompany a |
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| [608] | 98 | publication, this sort of documentary information certainly should be |
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| 99 | supplied, so that the CIF has value for archival and database purposes. |
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| 100 | If a CIF is being prepared for submission to |
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| 101 | an <I>Acta Crystallographia</I> journal, the IUCr has |
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| 102 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=ftp://ftp.iucr.org/pub/rietform.cif"> |
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| 103 | template with a recommended list of CIF data items. |
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| 104 | </A> |
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| 105 | This template has been utilized for creation of the template files |
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| 106 | distributed with GSAS/EXPGUI. |
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| 107 | <P> |
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| 108 | <H5>Template Files</H5> |
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| 109 | Since the GSAS2CIF program cannot obtain much of the information needed |
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| 110 | to create a CIF that documents a structural determination, |
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| 111 | this information must be supplied by the person running the program in |
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| 112 | the form of template files. |
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| 113 | The GSAS2CIF program simply copies this information |
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| 114 | from template files into the CIF created by GSAS2CIF. |
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| 115 | Three separate template files are |
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| 116 | used with GSAS2CIF: |
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| 117 | <OL> |
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| 118 | <LI>one with publication and other overall information, |
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| 119 | <LI> one with information about the sample & specimen and |
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| 120 | <LI> one with information about diffraction instrumentation and |
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| 121 | data collection parameters. |
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| 122 | </OL> |
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| 123 | Note that as distributed, these files do not contain any information, |
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| 124 | but rather define a set of suggested fields where the user can provide |
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| 125 | this information. Since much of the information in these fields will |
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| 126 | be the same for all CIF's prepared by a researcher or using a specific |
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| 127 | instrument, it will be a good idea to create customized versions of |
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| 128 | these template files and thus |
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| 129 | avoid inputing the same information multiple times. |
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| 130 | <P> |
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| 131 | When GSAS2CIF is used to create a CIF file for an experiment named |
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| 132 | <I>expnam</I> (e.g. from file <I>expnam</I>.EXP), the GSAS2CIF program |
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| 133 | creates CIF file <I>expnam</I>.cif containing GSAS results. Information |
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| 134 | from a series of template files is copied directly into the CIF. There will |
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| 135 | be N+M+1 template files, where N is the number of phases and M is the number |
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| 136 | of data histograms. The files are named as follows: |
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| 137 | <OL> |
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| 138 | <LI><I>expnam</I>_publ.cif for the publication/overall information template file; |
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| 139 | <LI><I>expnam</I>_phase<U>n</U>.cif for the N sample/specimen template file(s); |
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| 140 | <LI><I>expnam</I>_<I>INST</I><U>mm</U>.cif for the |
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| 141 | the M instrument/data sample/specimen template file(s), where <I>INST</I> is the instrument name |
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| 142 | (<a href="#iname">see below</a>). |
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| 143 | </OL> |
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| 144 | If these files do not exist, they are created and filled |
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| 145 | with the contents of master versions of the template files. |
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| 146 | In the case of the |
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| 147 | <I>expnam</I>_publ.cif and <I>expnam</I>_phase<U>n</U>.cif files, |
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| 148 | template files named template_publ.cif and template_phase.cif |
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| 149 | are read, if present from the same directory where the <I>expnam</I>.EXP |
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| 150 | file is found, and if not present there, from the GSAS data directory. |
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| 151 | In the case of the <I>expnam</I>_<I>INST</I><U>mm</U>.cif file(s), the |
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| 152 | program first looks for files named template_<I>INST</I>.cif in the |
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| 153 | current directory and the GSAS data directory and if that file is not |
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| 154 | found, file template_instrument.cif is read from the current directory |
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| 155 | and if not found, the GSAS data directory. |
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| 156 | This somewhat complex series of template files allows for the creation |
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| 157 | default template files for commonly-used instruments as well as the |
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| 158 | potential for reuse of the other template files, by copying these files |
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| 159 | as needed and also allows the GSAS2CIF program to be reused to update |
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| 160 | the CIF as needed without loss of input information. |
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| 161 | |
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| 162 | <P><B>Note</B>, that users should avoid editing the |
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| 163 | final <I>expnam</I>.cif file, but rather should edit the |
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| 164 | <I>expnam</I>_*.cif template files and then rerun GSAS2CIF to incorporate |
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| 165 | the revised template files into a new version of the <I>expnam</I>.cif file. |
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| 166 | In this way, if GSAS2CIF is rerun at a later time, |
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| 167 | the crystallographic results in the .CIF are updated and the |
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| 168 | template information is retained automatically. |
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| 169 | This editing can be done with any ASCII text editor, but an application |
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| 170 | has been included within EXPGUI, |
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| 171 | <a href="#filltemplate">FillTemplate</A>, for this purpose. |
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| 172 | <P> |
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| 173 | <H5>Other Input Files</H5> |
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| 174 | In addition to the reading the GSAS experiment file (file <I>expnam</I>.EXP), |
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| 175 | GSAS2CIF also reads the variance-covariance matrix created in GENLES |
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| 176 | (from file <I>expnam</I>.CMT) and a table of interatomic distances and angles |
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| 177 | created from program DISAGL (file <I>expnam</I>.DISAGL). If these files |
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| 178 | cannot be read, GSAS2CIF produces a warning message, since the CIF will be |
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| 179 | incomplete without this information. |
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| 180 | Note that the .CMT and .DISAGL are both derived from GENLES output and thus |
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| 181 | the .EXP file must have been used to run GENLES and then DISAGL just prior to |
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| 182 | running GSAS2CIF. If you edit the .EXP file or go back to |
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| 183 | an archived experiment file and do not rerun GENLES and then DISAGL, |
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| 184 | (<I>expnam</I>.O<I>nn</I>), the most recent <I>expnam</I>.CMT and |
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| 185 | <I>expnam</I>.DISAGL will be out-of-sync with the .EXP contents. GSAS2CIF |
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| 186 | will try to spot this and warn you, but some errors may be hard to catch. |
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| 187 | </BLOCKQUOTE> |
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| 188 | <a name="iname"></a><H4>Instrument Name</H4> |
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| 189 | <BLOCKQUOTE> |
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| 190 | An instrument name is needed for every GSAS histogram. It is best if this |
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| 191 | name is unique to a specific instrument, so for commercial instruments, |
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| 192 | it is best if this name contains part of the instrument serial number |
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| 193 | or the institution name, etc. |
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| 194 | The instrument name may be defined in the instrument parameter file, |
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| 195 | by inclusion of a record of type |
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| 196 | <Font type=fixed>"INS nn INAME </font><I>Instrument name</I>". |
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| 197 | If this name is not defined in the original instrument parameter file, |
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| 198 | when GSAS2CIF is run, it will request an instrument name for each histogram, |
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| 199 | and this information will be added to the GSAS experiment file. |
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| 200 | Note that the vertical bar character, (|), should not be used in instrument |
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| 201 | names. |
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| 202 | </BLOCKQUOTE> |
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| 203 | <a name="pubflag"> |
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| 204 | <H4>Publication/Non-Publish Flag for Distances and Angles</H4> |
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| 205 | </a> |
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| 206 | <BLOCKQUOTE> |
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| 207 | The DISAGL program will tabulate all interatomic distances within |
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| 208 | specified interatomic radii. These radii may be modified using EXPEDT |
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| 209 | (but not at present EXPGUI). All distances and angles listed by DISAGL in |
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| 210 | the <I>expnam</I>.LST file will be recorded in a more compact format in |
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| 211 | file named <I>expnam</I>.DISAGL. All these distances and angles will then be |
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| 212 | included in the CIF file when GSAS2CIF is run. |
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| 213 | <P> |
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| 214 | Note that when an IUCr journal publication is prepared from a CIF, these |
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| 215 | distances and angles are abstracted directly into the publication tables |
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| 216 | from the CIF, |
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| 217 | provided that a special CIF flag for each distance/angle |
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| 218 | (_geom_bond_publ_flag and _geom_angle_publ_flag) indicates that these values |
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| [610] | 219 | should be published. The character in the first column of the |
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| [608] | 220 | <I>expnam</I>.DISAGL indicates the value for this flag, when the |
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| [610] | 221 | distances/angles are tabulated in the CIF. If this character is anything |
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| 222 | other than "Y" or "y", the |
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| 223 | distance/angle is flagged as "do not publish". A value of "Y" or "y" |
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| 224 | indicates |
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| [608] | 225 | this flag should be set to "publish." At present, the only way to change this |
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| 226 | flag is manually, with a text editing program, such as wordpad or emacs. |
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| 227 | An EXPGUI program, |
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| [635] | 228 | <a href="#cifselect">CIFSelect</A>, is available for this chore. |
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| [608] | 229 | <P> |
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| [610] | 230 | When DISAGL is first run, this flag character is set to N (do not publish) |
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| [608] | 231 | for all distances and angles. However, if any of these flags are changed in |
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| 232 | the .DISAGL file, these flag settings will be retained if DISAGL is rerun. |
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| 233 | |
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| 234 | </BLOCKQUOTE> |
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| 235 | <a name="filltemplate"> |
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| [652] | 236 | <H2>The FillTemplate program</H2> |
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| [608] | 237 | <BLOCKQUOTE> |
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| 238 | </a> |
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| 239 | The EXPGUI FillTemplate program is used to edit the CIF template files |
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| 240 | used within GSAS2CIF. The <I>expnam</I>_*.cif files are edited by this |
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| 241 | program, if they exists. If these files are not found (because GSAS2CIF |
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| 242 | has not been run), the template_*.cif in the current directory are edited. |
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| 243 | If there these files are not found as well, the template_*.cif in the GSAS |
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| 244 | data directory are copied to the current directory and are then made available |
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| 245 | for editing. |
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| 246 | <P> |
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| 247 | The FillTemplate program is accessed in EXPGUI from the "CIF Export" submenu |
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| 248 | of the "Import/Export" menu. The FillTemplate program |
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| 249 | opens a window, as is shown below: |
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| 250 | </BLOCKQUOTE> |
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| [652] | 251 | </BLOCKQUOTE> |
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| [608] | 252 | <img src="ciffill1.gif" alt="View of FillTemplate window"> |
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| 253 | <BLOCKQUOTE> |
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| [652] | 254 | <BLOCKQUOTE> |
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| 255 | The box on the left side of the window displays the data names in the CIF |
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| [608] | 256 | as a hierarchical tree. Note that subentries can be displayed or hidden |
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| [652] | 257 | by clicking on the +/- sign to the right of each grouping. For example, |
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| 258 | by default the data names contained in each loop are not shown. |
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| 259 | However, clicking on the + sign to the right of the "loop_0" listing |
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| 260 | causes the data names in the loop to be shown (as in |
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| 261 | the <a href="#loopfig">example below</a>.) |
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| [608] | 262 | <P> |
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| [652] | 263 | Clicking on an individual data name causes the |
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| 264 | associated value to be displayed on the right. The value associated |
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| 265 | with the data name can be edited by |
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| 266 | clicking on the entry box. The information you enter is copied into the |
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| 267 | in-memory copy of the CIF when you click on another |
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| 268 | data name, etc. |
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| [608] | 269 | <P> |
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| [652] | 270 | In the example shown above, the data name |
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| 271 | <tt>_cell_measurement_temperature</tt> has been selected. |
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| 272 | This is defined in the |
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| 273 | CIF dictionary as a number |
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| 274 | between 0 and infinity with |
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| 275 | units of Kelvins. These units (K) are displayed adjacent to the entry box. |
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| 276 | When appropriate input is validated to require |
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| 277 | that valid numbers in the allowed range are input or that |
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| 278 | standard uncertainties (esd's) are entered only where allowed. |
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| 279 | Likewise, if the CIF dictionary defines a enumerated list of values |
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| 280 | for a data name, a menu button is offered in place of an entry box. In |
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| 281 | this way, only a valid entry from the list can be selected. |
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| [608] | 282 | <P> |
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| 283 | The controls on the bottom of the window have the following effects: |
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| 284 | |
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| 285 | <BLOCKQUOTE> |
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| 286 | <DL> |
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| 287 | <P><DT><B>Template file</B><DD> |
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| 288 | The menu button labeled "Template file" offers a list of template files. This |
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| 289 | button can be used to select a file to be edited. If changes have been made |
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| 290 | to the current CIF, that have not been saved to disk, the user is offered |
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| 291 | a chance to save or discard these changes. |
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| 292 | <P><DT><B>Next ? in template</B><DD> |
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| 293 | If the button labeled "Next ? in template" is pressed, |
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| 294 | the program scans forward |
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| 295 | in the current file, and if needed through subsequent files, for a data item |
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| 296 | where the value is a single question mark (?), since this value indicates |
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| 297 | a item where a value has not been specified. Note that the _journal_ |
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| 298 | data items, which are intended to be used by <I>Acta Crystallographia</I> |
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| 299 | editors, are ignored by this button. |
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| 300 | <P><DT><B>Exit</B><DD> |
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| 301 | The "Exit" button causes the program to exit. If any changes have been |
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| 302 | made to a data item or the CIF has been changed, but have not been saved, |
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| 303 | a chance is offered to save these items. |
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| [652] | 304 | <P><DT><a name="cifcontents"><B>Show (Hide) CIF contents</B></A><DD> |
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| [608] | 305 | The "Show CIF contents" button causes a window to be displayed |
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| 306 | that shows the text of the CIF, as shown below. As CIF data items |
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| 307 | are selected by clicking on data names or through use of the other buttons, |
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| 308 | the window is scrolled forward or backward to show the appropriate section. |
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| 309 | Note that it is possible to make editing changes directly to the CIF |
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| 310 | using this window, but the program cannot verify that these edits |
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| 311 | have the correct syntax. Further, the program will not note that changes |
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| 312 | have been made to the CIF |
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| 313 | so another section of the file must be changed, before the edits can be |
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| [652] | 314 | saved to disk (see the <a href="#saveedits">Save</a> button). |
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| [608] | 315 | <P> |
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| 316 | After the "Show CIF contents" button is pressed, the label changes to |
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| 317 | "Hide CIF contents"; pressing the button again causes the window to be hidden. |
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| 318 | <BR> |
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| 319 | <img src="cif_contents.gif" alt="View of CIF text window"> |
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| [652] | 320 | <P><DT><B>Show (Hide) CIF definitions</B><DD> |
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| 321 | As CIF data names are selected, their definitions are shown in the |
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| [608] | 322 | CIF Definitions window, as shown below. |
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| 323 | After the "Show CIF definitions" button is pressed, the label changes to |
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| 324 | "Hide CIF definitions"; pressing the button again causes the |
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| 325 | window to be hidden. |
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| 326 | <BR> |
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| 327 | <img src="cifdef.gif" alt="View of CIF definitions window"> |
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| [652] | 328 | |
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| 329 | <P><DT><a name="undo"><B>Undo</B></a><DD> |
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| 330 | As changes are made to the CIF template, they are recorded and can be |
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| 331 | reversed using the "Undo" button. There is no limit to the number of changes |
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| 332 | that are recorded. However, changes cannot be undone after the CIF has been |
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| 333 | saved to disk. |
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| 334 | <P><DT><a name="redo"><B>Redo</B></a><DD> |
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| 335 | If changes have been reversed with the <a href="#undo">"Undo"</a> button, |
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| 336 | the changes can be |
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| 337 | reapplied using the "Redo" button. The list of changes available for "Redo" |
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| 338 | is cleared when a new edit is made or when the CIF is saved. |
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| 339 | |
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| 340 | <P><DT><a name="saveedits"><B>Save</B></a><DD> |
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| [608] | 341 | Changes made to the CIF are not saved to the disk file automatically, |
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| 342 | unless the <a href="#autosave">Auto-Save</a> checkbutton is set. When changes |
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| 343 | have been made, but not saved to disk, this button is made active. |
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| 344 | <P><DT><a name="autosave"><B>Auto-Save</B></a><DD> |
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| 345 | When the Auto-Save mode is not selected, |
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| 346 | changes made to the in-memory copy of the CIF that is displayed in the |
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| 347 | <a href="#cifcontents">CIF Contents window</a> are not written to |
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| [652] | 348 | the disk file until the "<a href="#saveedits">Save</a>" |
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| [608] | 349 | button is pressed. If the |
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| 350 | Auto-Save mode is selected, these changes are saved to disk automatically. |
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| 351 | </DL> |
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| 352 | </BLOCKQUOTE> |
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| [652] | 353 | <H3>CIF loops</H3> |
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| 354 | <P> |
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| 355 | CIF loops allow multiple values to be associated with one or more data items, |
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| 356 | in effect defining a table of data. |
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| 357 | Clicking on a loop, causes all the data names in the loop to be displayed, |
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| 358 | as is shown below. |
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| 359 | </BLOCKQUOTE> |
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| 360 | </BLOCKQUOTE> |
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| 361 | <a name="loopfig"></a> |
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| 362 | <img src="ciffill.gif" alt="View of FillTemplate window"> |
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| 363 | <BLOCKQUOTE> |
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| 364 | <BLOCKQUOTE> |
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| 365 | When a loop is displayed, extra controls appear, as are defined below. |
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| 366 | <BLOCKQUOTE> |
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| 367 | <DL> |
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| 368 | <P><DT><a name="loopspinbox"><B>Loop element #</B></a><DD> |
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| 369 | The Loop element #" spinbox" is used to select |
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| 370 | which "row" from the loop is displayed. The up arrow advances to the next |
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| 371 | row, while the down arrow reverses by one entry. Numbers can also be typed into |
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| 372 | the entry box; the number is accepted when Enter is pressed. |
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| 373 | The keyboard up and down arrows can also |
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| 374 | be used to advance between entries. Other keys such as Page Up, Home, etc. |
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| 375 | advance in large increments. |
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| 376 | <P><DT><B>Add to loop</B><DD> |
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| 377 | A new row can be added to the end of a |
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| 378 | loop using the "Add to loop" button. The value for each new entry |
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| 379 | is initialized as "?" (meaning value unknown or unspecified.) |
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| 380 | <P><DT><B>Delete loop entry</B><DD> |
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| 381 | This deletes the current row from the loop. |
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| 382 | First select the row to delete with the |
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| 383 | "<a href="#loopspinbox">Loop element #</A>" |
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| 384 | spinbox. Note that the values are displayed for confirmation before the |
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| 385 | delete operation is performed. |
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| 386 | It is not possible to delete all entries from a loop, so |
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| 387 | this button is disabled when a loop has only a single row defined. |
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| 388 | </DL> |
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| 389 | </BLOCKQUOTE> |
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| 390 | It is also possible to click on the data name for a item inside a loop, in this |
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| 391 | case, all entries for that data item in the loop |
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| 392 | are displayed (a column). |
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| [608] | 393 | |
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| [652] | 394 | |
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| [608] | 395 | </BLOCKQUOTE> |
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| 396 | <a name="cifselect"> |
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| [652] | 397 | <H2>The CIFSelect utility</H2> |
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| [608] | 398 | <BLOCKQUOTE> |
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| 399 | </a> |
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| [635] | 400 | The CIFselect utility is available within EXPGUI |
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| 401 | to view interatomic distances and |
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| 402 | angles generated by DISAGL and to set the CIF publication flags for these |
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| 403 | values. CIFselect is accessed in EXPGUI from the "CIF Export" submenu |
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| 404 | of the "Import/Export" menu. CIFselect opens two windows, one for controlling |
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| 405 | the program and one to display the distances. |
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| 406 | <P> |
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| 407 | <img src="cifsel1.gif" alt="View of CIFselect window" align="right"> |
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| 408 | The control window is shown to the right. The buttons on this window are |
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| 409 | described below. |
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| 410 | <BR clear=all> |
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| 411 | <DL> |
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| 412 | <P><DT><B>Select Phase</B><DD> |
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| 413 | This provides a list of phases. |
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| 414 | <P><DT><B>Select Atom</B><DD> |
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| 415 | This provides a list of atoms for the current phase. |
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| 416 | <P><DT><B>Response to Mouse Click</B><DD> |
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| 417 | When the mouse is clicked on a distance or angle (see below), |
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| 418 | the publication flag for the may be changed. The effect is dictated by |
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| 419 | the mode selected here. In "<B>Toggle</B>" mode the publication flag |
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| 420 | is set to the opposite of the previous value. In "<B>Set</B>" mode, |
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| 421 | the publication flag will be set to "Y" (publish), regardless of the |
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| 422 | previous state of the flag. |
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| 423 | In "<B>Clear</B>" mode, |
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| 424 | the publication flag will be set to "N" (do not publish), regardless of the |
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| 425 | previous state of the flag. |
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| 426 | <P><DT><B>Distance selection: select matching angles?</B><DD> |
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| 427 | When this option is set to Yes, the publication flag will be set to "Yes" for |
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| 428 | all angles where both the publication flags for the distances are also set |
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| 429 | to "Yes". This is illustrated in the window shown below. |
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| 430 | Note that the distance AL3-O6_a is set to be not published. The five angles |
|---|
| 431 | that involve atom O6_a were automatically set to be not published. |
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| 432 | If this option is set to Yes, turning |
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| 433 | on the publication flag for distance AL3-O6_a would cause the publication |
|---|
| 434 | flag to be set on as well. If this option is set to "No", angle flags |
|---|
| 435 | must be changed individually. |
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| [608] | 436 | |
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| [635] | 437 | <P><DT><B>Save</B><DD> |
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| 438 | This button causes the current flag settings to be saved in the |
|---|
| 439 | <I>expnam</I>.DISAGL file. |
|---|
| 440 | |
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| 441 | <P><DT><B>Export Tables</B><DD> |
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| 442 | This button creates a file with all |
|---|
| 443 | bond distances and angles for the current phase, formatted in the |
|---|
| 444 | arrangement used in the window below. Each entry is separated by a |
|---|
| 445 | comma, suitable for reading into spreadsheet programs. |
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| 446 | |
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| 447 | <P><DT><B>Exit</B><DD> |
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| 448 | This button causes CIFselect to exit. If there are unsaved changes |
|---|
| 449 | to publication flags, you will be given an opportunity to save or |
|---|
| 450 | discard these changes. |
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| 451 | </DL> |
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| 452 | |
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| 453 | <P> |
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| 454 | The distance and angle display window is shown below. The |
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| 455 | items that are selected for publication are highlighted in yellow. |
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| 456 | <BR> |
|---|
| 457 | <img src="cifsel2.gif" alt="View of CIFselect window" align="right"> |
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| 458 | <BR clear=all> |
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| 459 | |
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| 460 | |
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| 461 | |
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| 462 | |
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| [608] | 463 | </BLOCKQUOTE> |
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| [610] | 464 | <H3>Acknowledgments</H3> |
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| [608] | 465 | <BLOCKQUOTE> |
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| [610] | 466 | The GSAS2CIF program was written by Brian H. Toby, Robert B. Von Dreele and |
|---|
| [635] | 467 | Allen C. Larson. The distance/angle display format for CIFselect was |
|---|
| 468 | suggested by Lachlan Cranswick, based on SHELX. |
|---|
| [610] | 469 | <P>Richard L. Harlow first got me interested in the problem of a |
|---|
| [608] | 470 | universal file format for powder diffraction data, leading eventually to |
|---|
| 471 | my involvement with CIF and then this programming |
|---|
| 472 | effort. For all this, I may someday forgive him. |
|---|
| 473 | </BLOCKQUOTE> |
|---|
| 474 | <P> |
|---|
| 475 | |
|---|
| 476 | <BLOCKQUOTE> |
|---|
| 477 | <BLOCKQUOTE> |
|---|
| [635] | 478 | <hr noshade height=1> |
|---|
| 479 | <B>Quote:</B><BR><a name="ps"> |
|---|
| 480 | <CENTER> |
|---|
| 481 | "A Rietveld refinement is never perfected, merely abandoned." |
|---|
| [608] | 482 | Peter Stephens</a> |
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| [635] | 483 | </CENTER> |
|---|
| 484 | <hr noshade height=1> |
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| [608] | 485 | </BLOCKQUOTE> |
|---|
| 486 | </BLOCKQUOTE> |
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| 487 | <P> |
|---|
| 488 | <a name="CIFintro"> |
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| 489 | <H3>Appendix: A quick & incomplete introduction to CIF</H3> |
|---|
| 490 | </a><BLOCKQUOTE> |
|---|
| 491 | A CIF file consists of logical groups of information that are |
|---|
| 492 | called data blocks, |
|---|
| 493 | since each block is initiated by a label of form data_<I>label</I>. |
|---|
| 494 | In the simple case, where a single crystallographic model is determined |
|---|
| 495 | from a single diffraction dataset (histogram), the CIF can be a |
|---|
| 496 | single block. In the case where either multiple datasets (histograms) |
|---|
| 497 | or where multiple phases are used in the refinement, a CIF will |
|---|
| 498 | require several data blocks to describe the data and results. |
|---|
| 499 | <P> |
|---|
| 500 | CIF consists of a series of tags, called data names, and values |
|---|
| 501 | associated with these data names. Together the data name and value |
|---|
| 502 | are called a data item. A separate document, the CIF (or pdCIF) |
|---|
| 503 | dictionary defines the meaning of each data name. If a value does not |
|---|
| 504 | contain any spaces, may be specifed without quotes, but either single or |
|---|
| 505 | double quotes may be used to delimit strings. A data value of one ore more |
|---|
| 506 | lines is quoted with semicolon characters (;). The two semicolons must be |
|---|
| 507 | the first character on each line and the final semicolon is expected to be |
|---|
| 508 | followed by a white-space character such as a space or then end-of-line. |
|---|
| 509 | With the exception of semicolon delimiters, which must be the first |
|---|
| 510 | character of a line to be recognized, CIF treats multiple spaces, blank |
|---|
| 511 | lines and other "white-space" characters as a single space. |
|---|
| 512 | <P> |
|---|
| 513 | The following lines give examples of a few CIF data items. |
|---|
| 514 | <BLOCKQUOTE> |
|---|
| 515 | <BLOCKQUOTE> |
|---|
| 516 | <PRE> |
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| 517 | _pd_calc_method 'Rietveld Refinement' |
|---|
| 518 | |
|---|
| 519 | _cell_volume 1811.00(5) |
|---|
| 520 | |
|---|
| 521 | _symmetry_space_group_name_H-M "I a 3 d" |
|---|
| 522 | |
|---|
| 523 | _pd_proc_ls_background_function |
|---|
| 524 | ; GSAS Background function number 1 with 4 terms. |
|---|
| 525 | Shifted Chebyshev function of 1st kind |
|---|
| 526 | 1: 139.025 2: -11.5408 3: 9.75652 4: 3.90497 |
|---|
| 527 | ; |
|---|
| 528 | </PRE> |
|---|
| 529 | </BLOCKQUOTE> |
|---|
| 530 | </BLOCKQUOTE> |
|---|
| 531 | CIF also allows multiple values to be associated with a CIF data item. |
|---|
| [610] | 532 | This is done by preceding the data name with the keyword loop_. If |
|---|
| [608] | 533 | two or more data names follow the loop_ keyword, a table can be |
|---|
| 534 | constructed, as is shown in the following examples. |
|---|
| 535 | |
|---|
| 536 | <BLOCKQUOTE> |
|---|
| 537 | <BLOCKQUOTE> |
|---|
| 538 | <PRE> |
|---|
| 539 | loop_ _symmetry_equiv_pos_as_xyz |
|---|
| 540 | +x,+y,+z +z,+x,+y |
|---|
| 541 | +y,+z,+x +x+1/2,+y,-z+1/2 |
|---|
| 542 | |
|---|
| 543 | |
|---|
| 544 | loop_ |
|---|
| 545 | _atom_site_label |
|---|
| 546 | _atom_site_fract_x |
|---|
| 547 | _atom_site_fract_y |
|---|
| 548 | _atom_site_fract_z |
|---|
| 549 | Y1 0.125 0.0 0.25 |
|---|
| 550 | FE2 0.0 0.0 0.0 |
|---|
| 551 | AL3 0.375 0.0 0.25 |
|---|
| 552 | O4 -0.02946(5) 0.05385(5) 0.15068(6) |
|---|
| 553 | </PRE> |
|---|
| 554 | </BLOCKQUOTE> |
|---|
| 555 | </BLOCKQUOTE> |
|---|
| 556 | Finally, it should be pointed out that two values in CIF have special meanings. |
|---|
| 557 | If a value is supplied as a single period (.), the meaning is the |
|---|
| 558 | value is not defined or is inappropriate. If the value is a question mark |
|---|
| 559 | (?), this means that the value is unknown or not specified. |
|---|
| 560 | <P> |
|---|
| 561 | For more information, see: |
|---|
| 562 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.iucr.org/iucr-top/cif/"> |
|---|
| 563 | The CIF home page</A>; short intros to |
|---|
| 564 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.iucr.org/iucr-top/cif/powder-announce.html"> |
|---|
| 565 | pdCIF</A> |
|---|
| 566 | & |
|---|
| 567 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.iucr.org/iucr-top/cif/powder-intro.html"> |
|---|
| 568 | CIF syntax</A> |
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| 569 | |
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| 570 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 571 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 572 | </TH><TH><A Href="excledt.html">Previous page</A> |
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| 573 | </TH></TR></TABLE><BR CLEAR=ALL> |
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| 574 | |
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| 575 | </BLOCKQUOTE> |
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| 576 | |
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| 577 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
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| 578 | <font size=-1><? lastmod(); ?></font> |
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| 579 | $Revision: 652 $ $Date: 2009-12-04 23:09:45 +0000 (Fri, 04 Dec 2009) $ |
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| 580 | </font> |
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| 581 | </BLOCKQUOTE> |
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| 582 | |
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| 583 | </BODY> |
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| 584 | </HTML> |
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