Changeset 1164
 Timestamp:
 Aug 17, 2011 9:13:48 AM (10 years ago)
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 branches/sandbox/doc
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branches/sandbox/doc/expgui6A.html
r1151 r1164 28 28 <center><h1> 29 29 <HR noshade width="75%" size="2" align="center"> 30 EXPGUI, part 6A30 EXPGUI, part 7 31 31 <HR noshade width="75%" size="2" align="center"> 32 32 </h1></center> 33 33 34 <h3>A. 6A Rigid Body Constraints panel</h3>34 <h3>A.7 Rigid Body Introduction</h3> 35 35 <DL><DL> 36 36 GSAS Rigid bodies are another way to constrain relative atomic 37 positions. This will be documented further in the future. 37 positions. In a rigid body fit, 38 a group of atoms are constrained so that they rotate and/or translate as a unit. 39 GSAS allows quite complex rigid bodies, with up to 9 scaling parameters and 40 when multiple rigid bodies are used with grouped parameters even more complex 41 constraints can be developed. The EXPGUI rigid body interface allows access to 42 most of the GSAS features and offers some setup features not in GSAS, but 43 expert users may need to use EXPEDT for some very complex constraint models. 44 <P> 45 Use of a rigid body reduces 46 the number of parameters refined, prevents deviations from chemical 47 reasonableness and generally helps obtain a more stable refinement. This can be especially important in the 48 early stages of refinement. Rigid 49 bodies are commonly used to constrain rigid moieties such phenyl or cyclopentadienyl rings but, they can be generated for much 50 more complicated structures. Rigid bodies in GSAS are always 51 represented by a set of Cartesian coordinates describing the relative positions 52 of the atoms to be constrained. More complex frameworks can be constructed 53 using multiple sets of Cartesian coordinates with variable multipliers, for 54 more complex constraints. Even more sophisticated refinements are possible when 55 multiple rigid bodies are constrained to share an origin or positioning (Euler) 56 angles. 57 <P> 58 Once created, the 59 rigid body framework is applied as a constraint by mapping it onto atoms in a 60 phase. The same rigid body framework can be mapped multiple times into one or 61 more phases. 62 Once mapped, the set 63 of atoms will refine as a single body with 3 parameters describing the 64 translation of the rigid body origin (generally the centroid of mass of the 65 atomic grouping but, this is optional) and 3 parameters describing the rotation 66 of the body about the origin (Euler Angles). TLS terms (translation, libration, 67 screw) can be used to model cooperative thermal motion about the rigid 68 body. The EXPGUI rigid body routines 69 will allow the user to readily generate the rigid body framework (called matrices 70 in EXPGUI terminology) and map the rigid body to sets of atoms already present 71 in the GSAS EXP file. 72 73 The EXPGUI Rigid Body Panel allows for the 74 creation or viewing of rigid bodies. 75 A rough outline of the procedure to generate and refine with a rigid body 76 is as follows: 77 78 <OL> 79 <LI>Define the framework of the rigid 80 body with a set of Cartesian coordinates representing the relative atomic 81 positions. This can be done by 82 manual input, loading the coordinates from an ASCII file, 83 converting Zmatrix coordinates to Cartesian or generating Cartesian coordinates 84 from fractional coordinates in an existing molecular fragment in the GSAS EXP 85 file. 86 <LI> 87 The rigid body 88 framework must be mapped upon the crystal structure. 89 This requires that the atoms in the 90 phase be sequential and must match the order of atoms in the rigid body 91 framework. 92 To change the sequential 93 order in the rigid body, the Edit Matrix routine may be used to reorder the 94 rigid body coordinates. 95 In the 96 mapping procedure, this number of the first atom in the phase to match the 97 rigid body is designated (since the mapping then follows) and both the Euler angles 98 and rigid body origin are specified; EXPGUI can help determine values 99 for these. 100 This can be repeated to map the rigid 101 body framework to other parts of the structure. 102 <LI> 103 Once the rigid body framework 104 is mapped to the crystal structure, the refinement flags for the Euler angles 105 and Origin can be set. This will turn on the 'X' refinement flags for the 106 included atoms in the Phase Panel. It is important that these match the state 107 of the rigid body refinement flags or GENLES will crash. 108 </OL> 109 </DL></DL> 110 <H3>A.7.a Main Rigid Body Panel</H3> 111 <DL><DL> 112 The main panel for rigid bodies presents a interface where bodies can 113 be initially defined. When bodies have been defined, a tab appears 114 for each defined body, where these bodies can be used or 115 edited. This main panel is shown below and subsequent sections 116 describe how bodies are initially defined. 117 <BR><img src="rb001.jpg" alt="RB start panel"> 118 <BR> 119 Rigid bodies are created 120 from one or more sets of Cartesian coordinates multiplied by a scale factor and 121 then summed to create Cartesian coordinates in Angstroms. This can be expressed 122 as a linear algebra expression, 123 <P><DL><DL> 124 XYZ = M1*XYZ1 + M2*XYZ2 + ... 125 </DL></DL> 126 <P> 127 Where XYZ, XYZ1, ...are 3 by N matrices (3 columns by N atoms) and M1, 128 M2,... 129 are scalars. Therefore in EXPGUI terminology, each set of Cartesian 130 coordinates is called a "Matrix." The 131 sum of these scaled matrices describes the rigid body framework that is to be 132 mapped upon the atoms of the crystal structure. Most commonly, however, only 133 one matrix is used and M1=1. In this case the matrix is simply a set of Cartesian 134 coordinates in Angstroms, which can be input by multiple methods. 135 As a reminder, note that the rigid body 136 framework will be mapped to consecutive atoms in the EXP file must be so the Cartesian 137 coordinates of the rigid body MUST be listed in a corresponding order. 138 <P> 139 If the ordering of the Cartesian 140 coordinates of the rigid body, as input, is incorrect, they may be rearranged 141 with the Edit Matrix panel invoked 142 from the Rigid Body Type panel. 143 <P> 144 Advanced refinements 145 may take advantage of the GSAS feature of multiple matrices, each with its own 146 matrix multiplier. This can result is some very advanced refinements such as 147 independently refining the CC and CH bond distances in a hydrocarbon 148 ring. 149 <P> 150 The "Create Rigid Body" tab offers several ways to create a rigid 151 body: 152 <UL><LI>Manual rigid body definition 153 <LI>Cartesian coordinates from ASCII text file 154 <LI>Cartesian coordinates from a Zmatrix 155 <LI>Compute Cartesian coordinates from EXP file (fractional coordinates) 156 </UL> 157 158 <H4>A.7.a1 Manual rigid body definition</H4> 159 <DL> 160 The manual definition window allows input of coordinates and 161 multipier(s) by typing values into boxes. Number of matrices 162 determines the number of multipliers and sets of coordinates that 163 are added. Number of Cartesian sites is the number of atoms in the 164 rigid body. The "Save Rigid Body" button creates a new rigid body 165 with the specified input. The "Export Cartesian Coordinates..." 166 writes an ASCII file with the current input. 167 <BR><img src="rb002.jpg" alt="Manual RB creation window"> 168 </DL> 169 <H4>A.7.a2 Cartesian coordinates from ASCII text file</H4> 170 <DL> 171 Cartesian coordinates 172 can be read from any ASCII file containing Cartesian coordinates in a standard 173 tabular format. 174 This routine allows 175 the user to determine which columns (separated by a delimiter) represents the X, 176 Y and Z coordinates. 177 The user also 178 has the option to ignore any row or column that contains irrelevant 179 information. 180 Once the Cartesian 181 coordinates are isolated, and the "Continue" button is pressed, 182 the user continues to the "Create Rigid Body" window (see above). 183 <BR><img src="rb003.jpg" alt="ASCII RB input window"> 184 </DL> 185 186 <H4>A.7.a3 Cartesian coordinates from a Zmatrix</H4> 187 <DL> 188 Cartesian coordinates 189 can also be calculated from a Zmatrix in an appropriate ASCII format. 190 The conversion routine will allow dummy 191 atoms to be identified and ignored in the conversion process. 192 Upon pressing the "Continue" button, the Zmatrix 193 is converted to Cartesian coordinates and the user progresses to the 194 "Create Rigid Body" window (see above). 195 <BR><img src="rb004.jpg" alt="Zmatrix RB input window"> 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). 204 Once the number of atoms in the body is 205 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 209 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 xaxis 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 215 ASCII text file (with the "Export Cartesian Coordinates" 216 button). 217 <BR><img src="rb005.jpg" alt="Fraction Coords RB input window"> 218 </DL> 219 220 </DL></DL> 221 <H3>A.7.b Rigid Body Panel</H3> 222 <DL><DL> 223 As each rigid body is 224 defined, a "Rigid Body Type N" panel will be created.<span 225 style="msospacerun:yes"> 226 This panel will show how the rigid body 227 is mapped, and will allow the user to map / unmap the 228 rigid body on to the crystal structure, view the rigid body (this 229 assumes the 230 <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A> program is installed on their computer), edit the 231 rigid body, set refinement flags, or delete the rigid body. 232 <BR><img src="rb006.jpg" alt="RB edit panel"> 233 234 <H4>A.7.b1 Plot Rigid Body</H4> 235 <DL> 236 <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A> 237 is a very useful viewing program that 238 EXPGUI can invoke, if installed. It 239 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. 242 <BR><img src="rb007.png" alt="DRAWxtl screen"> 243 </DL> 244 245 <H4>A.7.b2 Map Rigid Body</H4> 246 <DL> 247 The rigid body must be mapped to the 248 crystal structure to define the constraint. This is done by pressing 249 the "Map Rigid Body" button, which raises the window below. 250 <BR><img src="rb008.png" alt="Map RB"><BR> 251 In order to map the rigid body the user 252 will need to specify the phase and the sequence number of the first atom in the 253 .EXP file to be included. 254 This will 255 be the atom assigned to the first set of coordinates in the rigid 256 body. 257 Each succeeding atom will be assigned 258 the consecutive set of coordinates. 259 The origin and Euler angles for the rigid body placement must be 260 determined; this can be done by fitting to the atoms in the 261 .EXP file using the "Fit rigid body to phase" button. A 262 table of RMS (~ A distances) between the mapped rigid body placement 263 and the initial atom placements  this describes the quality of the fit. 264 If the fit is poor, it is 265 likely that the ordering of Cartesian coordinates is incorrect, resulting in high 266 RMS values. If this occurs, the ordering of the Cartesian coordinates must be 267 modified with the Edit Matrix routine. 268 <BR><img src="rb010.png" alt=""><BR> 269 <img src="rb009.png" alt="" ALIGN="RIGHT"> 270 The fit can be visually examined with 271 the "Plot rigid body & phase" button with results as 272 show to the right. 273 The rigid body is shown in 274 red and the .EXP file coordinates are shown in green. Note that it is often 275 easier to understand what is being plotted, when bonds are drawn. The input in 276 the "Bonds" box specifies ranges of distances where 0.91.1, 1.31.6 draws bonds 277 between atoms spaced 0.9 to 1.1 A (typical CH bonds) and 1.3 to 1.6 A (typical 278 organic molecule bonds). You may wish to specify different 279 ranges where other types of bonding are present. One can also change 280 the display from the DRAWxtl menus. 281 <BR Clear="all"> 282 </DL> 283 <H4>A.7.b3 Edit Rigid Body</H4> 284 <DL> 285 286 Pressing the "Edit Matrix" button on the "Rigid Body Type N" panel 287 provides an interface that will allow the Cartesian coordinates to be modified by 288 sorting, swapping, adding or deleting matrix elements. 289 It will also allow for setting the refinement flag for Matrix 290 Multipliers. 291 <BR><img src="rb011.jpg" alt=""><BR> 292 <img src="rb012.png" alt="" ALIGN="RIGHT"> 293 Note that repeating the previous 294 mapping, after reordering 295 of the Cartesian coordinates, the following fit of a cyclopentadienyl 296 ligand is accomplished and the RMS differences in the 297 fitting procedure are small. 298 Below 299 shows the correct fit. 300 <BR><img src="rb013.png" alt=""><BR> 301 <BR><img src="rb014.png" alt=""><BR> 302 </DL> 303 304 </DL></DL> 305 <H3>A.7.c Setting Rigid Body Refinement Flags</H3> 306 <DL><DL> 307 The "Refinement Flags" button opens a window that allows the 308 user to set flags to refine various parameters. 309 Parameters can be set up to refine as 310 free variables or constrained variables. 311 The TLS (translation, librations, screw) terms describe the rigid body 312 thermal motions and are normally off. 313 They should only be turned on if the user has a strong understanding of 314 the relationships between the TLS terms. 315 Note: if an Origin or Euler angle 316 flag is enabled, the appropriate atom X refinement flag on the phase panel will 317 be set. 318 GENLES will have errors if 319 rigid body parameters are refined, but not the positions of the corresponding 320 atoms. 321 322 Note that in EXPEDT, 323 rigid body parameters can be grouped by assigning them the same variable 324 number. The same feature is possible via a graphical interface by "tagging" (pressing 325 the appropriate button for) items to vary and then using the following buttons: 326 <UL><LI> 327 "Set Free Variables"  will assign each tagged parameter as 328 an unconstrained variable by providing a unique variable number. 329 330 <LI>Do Not Refine Variables  will turn off the refinement flag 331 for all tagged parameters. 332 333 <LI>Set Constrained variables  will constrain all tagged parameters 334 and assign a single variable for refinement. 335 <LI>Clear All Variables  will clear all refinement flags. 336 337 <LI>Assign Variables and Save  will assign variable numbers to each 338 unique parameter to be refined and close the Refinement Flag window. 339 <BR><img src="rb015.png" alt=""><BR> 340 <BR><img src="rb016.png" alt=""><BR> 341 342 The above Phase Panel shows the 'X' 343 refinement flags active allowing the rigid body refinement to 344 commence. 345 These flags were set automatically when 346 the rigid body position parameter were set to be refined. If these flags are 347 turned off, it is likely that GENLES will crash. 38 348 39 349 </DL></DL> 
branches/sandbox/doc/expgui7.html
r1150 r1164 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. 7Preferential Orientation Panel</h3></a>34 <h3>A.8 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. 7.a MarchDollase</H4>45 <h4>A.8.a MarchDollase</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. 7.b Spherical harmonic</H4>69 <H4>A.8.b Spherical harmonic</H4> 70 70 <DL><DL> 71 71 The spherical harmonic formulation, also referred to as an "orientation
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