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a [2009/08/06 14:35] – created clare | a [2022/11/03 15:08] (current) – external edit 127.0.0.1 | ||
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+ | ====== a ====== | ||
+ | **[//a// E] [//b// E] [//c// E] [//al// E] [//be// E] [//ga// E]** | ||
+ | |||
+ | Lattice parameters in Angstroms and lattice angles in degrees. | ||
+ | |||
+ | **[// | ||
+ | |||
+ | //adps// when used generates the //unn// atomic displacement parameters with considerations made for special positions. On termination of refinement the //adps// keyword is replaced with the //unn// parameters; see example AE1-ADPS.INP. Instead of using the //adps// keyword the //unn// parameters can be manually entered. | ||
+ | |||
+ | The //unn// matrix can be kept positive definite with the site dependent macro ADPs_Keep_PD; | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Signals that the associated phase is amorphous when calculating // | ||
+ | |||
+ | ** [// | ||
+ | |||
+ | Generates the un-normalized and normalized A and correlation matrices. If // | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Appends site fractional coordinates in Cartesian or fractional coordinates respectively to the *.OUT file at the end of a refinement. For the case of // | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Appends bond lengths to the end of the *.OUT file at the end of refinement. A number corresponding to equivalent positions is appended to site names. | ||
+ | |||
+ | // | ||
+ | |||
+ | An example of bond lengths output is as follows: | ||
+ | |||
+ | Y1:0 O1:0 2.23143 | ||
+ | |||
+ | O2:0 2.23143 88.083 | ||
+ | |||
+ | O3:0 2.28045 109.799 99.928 | ||
+ | |||
+ | The first line gives the distance between the sites Y1 and O2. The first number in the second line gives the distance between sites Y1 and O2. The third number of 88.083 gives the angle between the vectors Y1 to O1 and Y1 to O2. The first number on the third line contains the distance between sites Y1 and O3. The second number in the third line contains the angle between the vectors Y1 to O3 and Y1 to O2. The third number in line three contains the angle between the vectors Y1 to O3 and Y1 to O1. Thus bond lengths correspond to the first number in each line and bond angles start from the second number. The numbers after the site name and after the ‘:’ character corresponds to the site equivalent position as found in the *.SG space group files found in the SG directory | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | See section 5.2 for a description of // | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | ** [// | ||
+ | |||
+ | **// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Defines an atomic interaction with the name N between [[# | ||
+ | |||
+ | For // | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | When // | ||
+ | |||
+ | // | ||
+ | |||
+ | atomic_interaction... | ||
+ | |||
+ | ai_exclude_eq_0 | ||
+ | |||
+ | ai_sites_1 Pb | ||
+ | |||
+ | ai_sites_1 “O1 O2” | ||
+ | |||
+ | the following interactions are considered: | ||
+ | |||
+ | Pb:0 and O1: | ||
+ | |||
+ | Pb:0 and O2: | ||
+ | |||
+ | where the number after the ‘:’ character corresponds to the equivalent positions of the sites. | ||
+ | |||
+ | // | ||
+ | |||
+ | **__Functions__** | ||
+ | |||
+ | The // | ||
+ | |||
+ | AI_R(#ri): Returns the distance between the current site and the atom defined with Ri = #ri. | ||
+ | |||
+ | AI_R_CM: A function of no arguments that returns the geometric center of the current atom and the atoms defined in $sites_2. | ||
+ | |||
+ | AI_Flatten(# | ||
+ | |||
+ | AI_Cos_Angle(# | ||
+ | |||
+ | AI_Angle(# | ||
+ | |||
+ | Examples BENZENE_AI1.INP, | ||
+ | |||
+ | // | ||
+ | |||
+ | atomic_interaction ai1 = | ||
+ | |||
+ | IF R < 3 THEN | ||
+ | |||
+ | (R-3)^2 | ||
+ | |||
+ | ELSE | ||
+ | |||
+ | 0 | ||
+ | |||
+ | ENDIF | ||
+ | |||
+ | ; | ||
+ | |||
+ | ai_exclude_eq_0 | ||
+ | |||
+ | ai_sites_1 C* | ||
+ | |||
+ | ai_sites_1 C* | ||
+ | |||
+ | ai_radius 3 | ||
+ | |||
+ | penalty = If(Cycle_Iter < 10, ai1, 0); | ||
+ | |||
+ | This example demonstrates anti-bumping between molecules for the first ten iterations of a [[# | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Used for writing //site// dependent details to file. See the keyword //out// for a description of // | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Defines the full axial divergence model using the method of Cheary & Coelho (1998b). | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | The macro Full_Axial_Model simplifies the use of // |