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b [2009/08/27 11:11] – clare | b [2022/11/03 15:08] (current) – external edit 127.0.0.1 | ||
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+ | ====== b ====== | ||
+ | **[//bkg// [@] # # #...]** | ||
+ | |||
+ | Defines a Chebyshev polynomial where the number of coefficients are equal to the number of numeric values appearing after the //bkg// keyword. | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | **[// | ||
+ | |||
+ | // | ||
+ | |||
+ | // | ||
+ | |||
+ | Parameter values used at the start of each refinement cycle are obtained from the end of the first refinement cycle. // | ||
+ | |||
+ | If // | ||
+ | |||
+ | Parameter values obtained at the end of each bootstrap refinement cycle is written to disk in binary format. These values are then read and processed at the end of the bootstrap process without actually storing all of the values in memory. Thus the bootstrap process has a small memory footprint. | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Defines a site interaction with the name N between [[# | ||
+ | |||
+ | When either //from_N// or //to_N// are defined, the interactions between $site_1 and $site_2 are sorted by distance and only the interactions between the //from_N// and //to_N// are considered. | ||
+ | |||
+ | // | ||
+ | |||
+ | For example, the following could be used to iterate from the nearest atom to the third atom from a site called Si1: | ||
+ | |||
+ | str | ||
+ | |||
+ | site Si1... | ||
+ | |||
+ | site O1... | ||
+ | |||
+ | site O2... | ||
+ | |||
+ | site O3... | ||
+ | |||
+ | box_interaction Si1 O* to_N 2 !si1o = (R-2)^2; | ||
+ | |||
+ | penalty = !si1o; | ||
+ | |||
+ | In this example the nearest three oxygen atoms are soft constrained to a distance of 2 Angstroms by the use of the penalty function. Counting starts at zero and thus //to_N// is set to 2 to iterate up to the third nearest atom. | ||
+ | |||
+ | The wild card character ‘*’ used in “O*” means that sites with names starting with ‘O’ are considered. In addition to using the wild card character, the site names can be explicitly written within double quotation marks, for example: | ||
+ | |||
+ | box_interaction Si1 “O1 O2 O3” to_N 3 etc... | ||
+ | |||
+ | Interactions between Si1 and the three oxygen atoms O1, O2, O3 may not all be included, for example, if Si1 had as its nearest neighbours the following: | ||
+ | |||
+ | Si1 ↔ O1,1 at a distance of 1.0 Angstroms | ||
+ | |||
+ | Si1 ↔ O2,3 at a distance of 1.1 Angstroms | ||
+ | |||
+ | Si1 ↔ O2,1 at a distance of 1.2 Angstroms | ||
+ | |||
+ | Si1 ↔ O1,2 at a distance of 1.3 Angstroms | ||
+ | |||
+ | then two equivalent positions of site O1 and two equivalent positions of O2 are included in the interaction equation; thus no interaction between Si1-O3 is considered. To ensure that each of the three oxygens had Si1 included in an interaction equation then the following could be used: | ||
+ | |||
+ | box_interaction “O1 O2 O3” Si1 to_N 0 etc… | ||
+ | |||
+ | Thus the order of $site_1 and $site_2 is important when either from_N or to_N is defined. | ||
+ | |||
+ | The reserved parameters Ri and Break can also be used in interaction equations when either from_N or to_N is defined. Ri returns the index of the current interaction being operated on with the first interaction starting at Ri=0. | ||
+ | |||
+ | // | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Breaks the current [[# | ||
+ | |||
+ | Example ALVO4-GRS.INP demonstrates the use of // | ||
+ | |||
+ | // | ||
+ | |||
+ | **[// | ||
+ | |||
+ | Used for applying the Brindley correction for spherical particles. The macro Apply_Brindley_Spherical_R_PD(R, | ||
+ | |||
+ | macro Apply_Brindley_Spherical_R_PD(R, | ||
+ | |||
+ | { | ||
+ | |||
+ | brindley_spherical_r_cm = (R) (PD); | ||
+ | |||
+ | } | ||
+ | |||
+ | R is the radius of the particle in cm and PD is the packing density, a number that is not updated and not refined. Here’s an example: | ||
+ | |||
+ | xdd... | ||
+ | |||
+ | str | ||
+ | |||
+ | Apply_Brindley_Spherical_R_PD(R, | ||
+ | |||
+ | MVW(0,0,0) | ||
+ | |||
+ | str | ||
+ | |||
+ | Apply_Brindley_Spherical_R_PD(R, | ||
+ | |||
+ | MVW(0,0,0) | ||
+ | |||
+ | Note, that PD is incorporated by way of an equation definition for // | ||
+ | |||
+ | The Brindley correction can be applied to all phases including //xo_Is//. In the case of phases that do not have lattice parameters or sites then the User would need to enter values for // | ||
+ | |||
+ | xo_Is | ||
+ | |||
+ | Apply_Brindley_Spherical_R_PD(.002, | ||
+ | |||
+ | MVW(654, 230, 0) | ||
+ | |||
+ | phase_MAC 200 |