Changeset 1218
- Timestamp:
- Aug 19, 2012 1:17:28 PM (8 years ago)
- Location:
- trunk/doc
- Files:
-
- 6 added
- 5 edited
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- Unmodified
- Added
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trunk/doc/expgui.html
r1166 r1218 51 51 <P> 52 52 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=CENTER> 53 <TR><TH BGCOLOR="#F0F0F0" rowspan= 3>GUI Sections</TH>53 <TR><TH BGCOLOR="#F0F0F0" rowspan=4>GUI Sections</TH> 54 54 <TH><A Href="expgui1.html">Least Squares</A></TH> 55 55 <TH><A Href="expgui2.html">Phase info</A></TH> … … 59 59 <TH><A Href="expgui4.html">Scaling info</A></TH> 60 60 <TH><A Href="expgui5.html">Profile terms</A></TH> 61 <TH><A Href="expgui6.html">Constraints & Restraints</A></TH>61 <TH><A Href="expgui6.html">Constraints</A></TH> 62 62 </TR> 63 63 <TR> 64 <TH><A Href="expgui6R.html">Restraints</A></TH> 64 65 <TH><A Href="expgui6A.html">Rigid Bodies</A></TH> 65 66 <TH><A Href="expgui7.html">Preferred Orientation</A></TH> 67 </TR> 68 <TR> 66 69 <TH><A Href="expguic.html">Menus</A></TH> 70 <TH> </TH> 67 71 <TH> </TH> 68 72 </TR> -
trunk/doc/expgui6.html
r1166 r1218 22 22 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> 23 23 <TR><TH><A Href="expgui.html">EXPGUI top</A> 24 </TH><TH><A Href="expgui6 A.html">Next page</A>24 </TH><TH><A Href="expgui6R.html">Next page</A> 25 25 </TH><TH><A Href="expgui5.html">Previous page</A> 26 26 </TH></TR></TABLE><BR CLEAR=ALL> … … 32 32 </h1></center> 33 33 34 <h3>A.6 Re/Constraints panel</h3> 35 <DL><DL> 36 GSAS offers two types of restraints that can be included in a model. 37 So called "soft constraints" or "restraints" penalize the fit if 38 aspects of a model (for example, bond lengths) differ from selected values. 39 So called "hard constraints" reduce the actual number of 34 <h3>A.6 Constraints panel</h3> 35 <DL><DL> 36 GSAS offers two ways to limit changes to parameters that are based rules 37 created by a crystallographer to create what is felt to be the most 38 reasonable model. 39 So called "soft constraints", which are better described as "restraints" 40 penalize the fit if 41 aspects of a model (for example, bond lengths) differ from selected 42 values. They are now located on the on the <A Href="expgui6R.html">Restraints panel</A>. 43 Actual constraints, which are sometimes called "hard constraints", are 44 on panel described here. They reduce the actual number of 40 45 parameters in a model, 41 46 by grouping parameters so that a single shift (possibly scaled) is 42 47 applied to each parameter in the group. 43 The Re/Constraints panel is used to set these "hard constraints" or in44 the case of bond distances, "restraints".45 48 At this time the only constraints that can be set in EXPGUI are on atomic 46 and profile profile (others can be set in EXPEDT). EXPEDT offers many 49 and profile profile (others can be set in EXPEDT). 50 EXPEDT offers many 47 51 other types of restraints as well. 48 52 <P> … … 51 55 if two atoms 52 56 are constrained so that the shift on their occupancy is the same, but 53 the initial occupancies differ, the in occupancy difference will not change54 as the values refine.57 the initial occupancies differ, the difference in their occupancies 58 will not change as the values are refined. 55 59 <P> 56 60 Due to the way GSAS implements constraints, a parameter can be included 57 61 in only one constraint. Should one or more parameters be constrained twice, 58 the refinement results are unpredictable. 62 the refinement results are unpredictable, so EXPGUI will not allow 63 this (EXPEDT will). One can sometimes bypass 64 this problem by defining redundant parameters. For example to 65 constrain the occupancy of site A to B and site A to C, one can 66 create two atom A sites: A<sub>1</sub> & A<sub>2</sub>. Then one can create two 67 constraints, for site A<sub>1</sub> to B and site A<sub>2</sub> to C. The actual occupancy 68 of site A is then that of A<sub>1</sub> plus A<sub>2</sub> 59 69 60 70 </DL></DL> … … 66 76 variable by clicking on the buttons at the top of the panel. 67 77 <P> 68 To delete one or more constraints, click on the appropriate checkbuttons in the <B>Delete</B> column and the press the Delete button, below. 78 To delete one or more constraints, click on the appropriate 79 checkbuttons 80 in the <B>Delete</B> column and the press the Delete button, below. 69 81 </DL></DL> 70 82 <img SRC="mc.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> … … 214 226 usually make sense and EXPGUI does not allow it. 215 227 </DL></DL> 216 <a name="DistanceRestraints"></a>217 <H4>Distance Restraints</H4>218 <DL><DL>219 When the distance restraints tab is first selected, the active220 distance restraints for the selected phase are shown. The <B>Atom 1</B> and221 <B>Atom 2</B> buttons can be used to sort this list.222 <P>223 The <B>Restraint Weight</B> parameter is very important. As this224 determines how strongly the distance restraints will be used in the225 refinement relative to the diffraction data. This value is sometimes226 set as high as 500,000 in the initial stages of a fit, but should be227 lowered as much as is possible in the final stages of the fit, as228 needed to obtain chemically plausible interatomic distances. For229 some refinements, a value of 0.0 is possible for the Restraint230 Weight in the final stages. This removes any restraint effect.231 232 To see how restraints are affecting the refinement, one can look at233 the ratio of the "Sum(w*d**2)" (shown in the .LST file) for the234 diffraction histograms vs. the restraint histogram.235 <P>236 The <B>Active Restraints Editor</B> can be used to select distances237 to be restrained or edit the restraints. If there are too many238 distances shown, the options at the top of the window can be used to239 select a distance range, or specific atoms to include. Likewise,240 only restrained or unrestrained distances can be selected. The241 changes are applied when the <B>Filter</B> button is pressed.242 <P>243 The bottom section of the window shows individual interatomic244 distances. A <B>Restraint</B> and <B>Tolerance</B> value is needed to restrain245 that distance. The quantity minimized is246 <blockquote>247 <blockquote>248 "Restraint Weight" * SUM{ [ (Distance - Restraint) / Tolerance ]**2 }249 </blockquote>250 </blockquote>251 thus the "Tolerance" provides individual weighting for each252 restraint.253 <P>254 To set a large number of restraints at the same time, select the255 check button next to the distance(s), or use the <B>Check256 All</B>. Then use the section above to enter a global257 <B>Restraint</B> and <B>Tolerance</B> value. These values are set258 when the <B>Set Checked</B> button is used. The <B>Delete259 Checked</B> button removes restraints from all selected distances.260 <P>261 The entered restraint information will be used onlt when the <B>Save262 Changes</B> button is pressed. The <B>Cancel</B> button will reverse263 any changes made while the window is open. Closing the window has264 the same effect as "Cancel."265 <P>266 Note that the interatomic distances that are shown are determined by267 the parameters to program DISAGL. These are controlled with the268 <B>Edit Search Distance Parameters</B> button.269 270 </DL></DL>271 228 <hr> 272 229 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> 273 230 <TR><TH><A Href="expgui.html">EXPGUI top</A> 274 </TH><TH><A Href="expgui6 A.html">Next page</A>231 </TH><TH><A Href="expgui6R.html">Next page</A> 275 232 </TH><TH><A Href="expgui5.html">Previous page</A> 276 233 </TH></TR></TABLE> -
trunk/doc/expgui6A.html
r1184 r1218 23 23 <TR><TH><A Href="expgui.html">EXPGUI top</A> 24 24 </TH><TH><A Href="expgui7.html">Next page</A> 25 </TH><TH><A Href="expgui6 .html">Previous page</A>25 </TH><TH><A Href="expgui6R.html">Previous page</A> 26 26 </TH></TR></TABLE><BR CLEAR=ALL> 27 27 28 28 <center><h1> 29 29 <HR noshade width="75%" size="2" align="center"> 30 EXPGUI, part 730 EXPGUI, part 8 31 31 <HR noshade width="75%" size="2" align="center"> 32 32 </h1></center> 33 33 34 <h3>A. 7Rigid Body Introduction</h3>34 <h3>A.8 Rigid Body Introduction</h3> 35 35 <DL><DL> 36 36 GSAS Rigid bodies are another way to constrain relative atomic … … 108 108 </OL> 109 109 </DL></DL> 110 <H3>A. 7.a Main Rigid Body Panel</H3>110 <H3>A.8.a Main Rigid Body Panel</H3> 111 111 <DL><DL> 112 112 The main panel for rigid bodies presents a interface where bodies can … … 156 156 </UL> 157 157 158 <H4>A. 7.a1 Manual rigid body definition</H4>158 <H4>A.8.a1 Manual rigid body definition</H4> 159 159 <DL> 160 160 The manual definition window allows input of coordinates and … … 167 167 <BR><img src="rb002.jpg" alt="Manual RB creation window"> 168 168 </DL> 169 <H4>A. 7.a2 Cartesian coordinates from ASCII text file</H4>169 <H4>A.8.a2 Cartesian coordinates from ASCII text file</H4> 170 170 <DL> 171 171 Cartesian coordinates … … 184 184 </DL> 185 185 186 <H4>A. 7.a3 Cartesian coordinates from a Z-matrix</H4>186 <H4>A.8.a3 Cartesian coordinates from a Z-matrix</H4> 187 187 <DL> 188 188 Cartesian coordinates … … 195 195 <BR><img src="rb004.jpg" alt="Z-matrix RB input window"> 196 196 </DL> 197 <H4>A.7.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4> 198 <DL> 199 Cartesian coordinates 200 can also be determined from atoms in the EXP file. 201 In order to generate Cartesian 202 coordinates, the number of sites in the rigid body framework must be specified 203 as well as the starting atom (remember rigid bodies are mapped consecutively). 197 <A name="fromEXP"> 198 <H4>A.8.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4> 199 </A> 200 <DL> 201 A rigid body can also be created directly by computing Cartesian coordinates 202 for atoms in the current EXP file. 203 In order to do this, the number of atom sites in the rigid body framework must be specified 204 as well as the starting atom number (remember rigid bodies are mapped 205 consecutively) using the window shown below. 204 206 Once the number of atoms in the body is 205 207 set, the "Choose Start Atom" button is pressed. This creates buttons for 206 all possible choices for the first atom to define the body. Once the starting 207 atom is selected by pressing one of these button(s), the atoms to be used to 208 define the rigid body framework have been determined. The user must than select 208 all possible choices for the first atom to define the body. The starting 209 atom is selected by pressing one of these button(s) and this defines 210 the atoms to be used in the rigid body framework. The user must then 211 select 209 212 which atoms will be used to define the origin (the origin will be at the 210 centroid of the atoms chosen) and must define the axes that will be used to 211 generate the x-axis and the xy plane. 212 The Cartesian coordinates can then be generated. 213 Either the defined body can be determined and mapped (with the "Save and Map 214 Rigid Body" button), or the Cartesian coordinates can exported to an 213 centroid of the atoms chosen) as well as define the axes that will be used to 214 generate the x-axis and the xy plane for the Cartesian coordinate system. 215 The Cartesian coordinates for the body that are generated can be exported to an 215 216 ASCII text file (with the "Export Cartesian Coordinates" 216 button). 217 <BR><img src="rb005.jpg" alt="Fraction Coords RB input window"> 217 button) for later use. More commonly, the "Save and Map 218 Rigid Body" button is used; this creates a new rigid body type and 219 maps that body (<A href="#MapBody">see A.8.b2</A>) to the selected atoms in the phase. 220 <BR><img src="rb005.jpg" alt="Fraction Coords RB input window"> 218 221 </DL> 219 222 220 223 </DL></DL> 221 <H3>A. 7.b Rigid Body Panel</H3>224 <H3>A.8.b Rigid Body Panel</H3> 222 225 <DL><DL> 223 226 As each rigid body is … … 232 235 <BR><img src="rb006.jpg" alt="RB edit panel"> 233 236 234 <H4>A. 7.b1 Plot Rigid Body</H4>237 <H4>A.8.b1 Plot Rigid Body</H4> 235 238 <DL> 236 239 <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A> … … 238 241 EXPGUI can invoke, if installed. It 239 242 allows for the viewing of the rigid body to ensure it is correct before mapping 240 and matches the ordering of the atoms in the EXP file. The plot below 241 was obtained from the "Plot Rigid Body" button. 243 and matches the ordering of the atoms in the EXP file. Note that plots 244 to not display atom types, since there is no type information 245 associated with position in a rigid body. Atom types are determined 246 by the atoms when the body is mapped. A sample plot 247 obtained from the "Plot Rigid Body" button is shown below. 242 248 <BR><img src="rb007.png" alt="DRAWxtl screen"> 243 249 </DL> 244 245 <H4>A. 7.b2 Map Rigid Body</H4>246 < DL>250 <A name="MapBody"> 251 <H4>A.8.b2 Map Rigid Body</H4> 252 </A><DL> 247 253 The rigid body must be mapped to the 248 254 crystal structure to define the constraint. This is done by pressing 249 255 the "Map Rigid Body" button, which raises the window below. 250 256 <BR><img src="rb008.png" alt="Map RB"><BR> 257 Note that when a rigid body is created from atoms already in the .EXP 258 file (<A href="#fromEXP">see A.8.a4</A>), the "Save and Map" command 259 performs this step automatically. 260 <P> 251 261 In order to map the rigid body the user 252 262 will need to specify the phase and the sequence number of the first atom in the … … 281 291 <BR Clear="all"> 282 292 </DL> 283 <H4>A. 7.b3 Edit Rigid Body</H4>293 <H4>A.8.b3 Edit Rigid Body</H4> 284 294 <DL> 285 295 … … 303 313 304 314 </DL></DL> 305 <H3>A. 7.c Setting Rigid Body Refinement Flags</H3>315 <H3>A.8.c Setting Rigid Body Refinement Flags</H3> 306 316 <DL><DL> 307 317 The "Refinement Flags" button opens a window that allows the … … 345 355 These flags were set automatically when 346 356 the rigid body position parameter were set to be refined. If these flags are 347 turned off, it is likely that GENLES will crash. 348 357 turned off, it is likely that GENLES will crash. Note that atoms in a 358 rigid body are now tagged with the letter "r" in the atom listings. 349 359 </DL></DL> 350 360 <hr> … … 352 362 <TR><TH><A Href="expgui.html">EXPGUI top</A> 353 363 </TH><TH><A Href="expgui7.html">Next page</A> 354 </TH><TH><A Href="expgui6 .html">Previous page</A>364 </TH><TH><A Href="expgui6R.html">Previous page</A> 355 365 </TH></TR></TABLE> 356 366 -
trunk/doc/expgui7.html
r1166 r1218 28 28 <center><h1> 29 29 <HR noshade width="75%" size="2" align="center"> 30 EXPGUI, part 830 EXPGUI, part 9 31 31 <HR noshade width="75%" size="2" align="center"> 32 32 </h1></center> 33 33 34 <h3>A. 8Preferential Orientation Panel</h3></a>34 <h3>A.9 Preferential Orientation Panel</h3></a> 35 35 <DL><DL> 36 36 The Preferential Orientation Panel is used to control parameters related … … 43 43 </DL></DL> 44 44 <a name="MD"></a> 45 <h4>A. 8.a March-Dollase</H4>45 <h4>A.9.a March-Dollase</H4> 46 46 <DL><DL> 47 47 In this model one or more axes are designated … … 67 67 </DL></DL> 68 68 <a name="ODF"></a> 69 <H4>A. 8.b Spherical harmonic</H4>69 <H4>A.9.b Spherical harmonic</H4> 70 70 <DL><DL> 71 71 The spherical harmonic formulation, also referred to as an "orientation
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