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manual_part_3 [2009/08/26 15:02]
clare
manual_part_3 [2009/08/27 09:54] (current)
clare
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 ====== 11       Charge-flipping ====== ====== 11       Charge-flipping ======
  
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 Perturbations can be categorized as being of either phase, structure factor intensity or electron density perturbations as shown in Table 11‑2. There are two built in flipping regimes, //​flip_regime_2//​ and //​flip_regime_3//,​ and one user defined regime //​flip_equation//​. Only one can be used and they all modify the electron density. In the absence of a flipping regime the following is used: Perturbations can be categorized as being of either phase, structure factor intensity or electron density perturbations as shown in Table 11‑2. There are two built in flipping regimes, //​flip_regime_2//​ and //​flip_regime_3//,​ and one user defined regime //​flip_equation//​. Only one can be used and they all modify the electron density. In the absence of a flipping regime the following is used:
  
-| <​sub>​{{Technical_Reference%20V4-1_files:​image171.gif?​175x48}}</​sub>​ | (11‑1) |+| <​sub>​{{techref_files:​image171.gif?​175x48}}</​sub>​ | (11‑1) |
  
 where //d// corresponds to the electron density threshold. where //d// corresponds to the electron density threshold.
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 The elctron density is modified according to Eq. (11‑1) and then further modified using: The elctron density is modified according to Eq. (11‑1) and then further modified using:
  
-<​sub>​{{Technical_Reference%20V4-1_files:​image173.gif?​264x28}}</​sub>//​flip_regime_2//​ is typically ramped from 1 to 0.+<​sub>​{{techref_files:​image173.gif?​264x28}}</​sub>//​flip_regime_2//​ is typically ramped from 1 to 0.
  
 **[//​flip_regime_3//​ !E]** **[//​flip_regime_3//​ !E]**
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 The elctron density is modified according to Eq. (11‑1) and then further modified using: The elctron density is modified according to Eq. (11‑1) and then further modified using:
  
-<​sub>​{{Technical_Reference%20V4-1_files:​image175.gif?​393x51}}</​sub>​A value of 0.5 for //​flip_regime_3//​ introduces little perturbation whilst reducing the occurance of uranium atom solutions. It is recommended that //​flip_regime_3//​ be used in cases where //​flip_regime_2//​ produces uranium atom solutions. An additional perturbation,​ such as “//​add_to_phases_of_weak_reflections//​=90;​” may be necessary.+<​sub>​{{techref_files:​image175.gif?​393x51}}</​sub>​A value of 0.5 for //​flip_regime_3//​ introduces little perturbation whilst reducing the occurance of uranium atom solutions. It is recommended that //​flip_regime_3//​ be used in cases where //​flip_regime_2//​ produces uranium atom solutions. An additional perturbation,​ such as “//​add_to_phases_of_weak_reflections//​=90;​” may be necessary.
  
 **[//​fraction_density_to_flip//​ !E]** **[//​fraction_density_to_flip//​ !E]**
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 The text output '​symmetry error' as displayed when //​symmetry_obey_0_to_1//​ is used is defined as follows: The text output '​symmetry error' as displayed when //​symmetry_obey_0_to_1//​ is used is defined as follows:
  
-'​symmetry error' = <​sub>​{{Technical_Reference%20V4-1_files:​image177.gif?​127x29}}</​sub>​+'​symmetry error' = <​sub>​{{techref_files:​image177.gif?​127x29}}</​sub>​
  
 where the summation is over all of the electron density grid points. where the summation is over all of the electron density grid points.
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 //​tangent_scale_difference_by//​ corresponds to //S// in the following: //​tangent_scale_difference_by//​ corresponds to //S// in the following:
  
-| <​sub>​{{Technical_Reference%20V4-1_files:​image179.gif?​210x25}}</​sub>​ <​sub>​{{Technical_Reference%20V4-1_files:​image181.gif?​76x25}}{{Technical_Reference%20V4-1_files:​image183.gif?​48x24}}</​sub>​ <​sub>​{{Technical_Reference%20V4-1_files:​image185.gif?​215x36}}</​sub>​  <​sub>​{{Technical_Reference%20V4-1_files:​image187.gif?​219x36}}</​sub>​ <​sub>​{{Technical_Reference%20V4-1_files:​image189.gif?​113x27}}</​sub>,​ <​sub>​{{Technical_Reference%20V4-1_files:​image191.gif?​100x31}}</​sub>​ | (1) |+| <​sub>​{{techref_files:​image179.gif?​210x25}}</​sub>​ <​sub>​{{techref_files:​image181.gif?​76x25}}{{techref_files:​image183.gif?​48x24}}</​sub>​ <​sub>​{{techref_files:​image185.gif?​215x36}}</​sub>​  <​sub>​{{techref_files:​image187.gif?​219x36}}</​sub>​ <​sub>​{{techref_files:​image189.gif?​113x27}}</​sub>,​ <​sub>​{{techref_files:​image191.gif?​100x31}}</​sub>​ | (1) |
  
 **[//​user_threshold//​ !E]** **[//​user_threshold//​ !E]**
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 view_cloud = Mod(Cycle_Iter,​ 10) == 0; view_cloud = Mod(Cycle_Iter,​ 10) == 0;
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 ====== 12       Indexing ====== ====== 12       Indexing ======
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 Defines //​X<​sub>​hh</​sub>//​ in the reciprocal lattice equation: Defines //​X<​sub>​hh</​sub>//​ in the reciprocal lattice equation:
  
-<​sub>​{{Technical_Reference%20V4-1_files:​image193.gif?​319x50}}</​sub>​In a triclinic lattice the highest d-spacing can probably be indexed as 100 or 200 etc. Thus+<​sub>​{{techref_files:​image193.gif?​319x50}}</​sub>​In a triclinic lattice the highest d-spacing can probably be indexed as 100 or 200 etc. Thus
  
 index_x0 = 1%%/​(%%d<​sub>​max</​sub>​)^2;​ index_x0 = 1%%/​(%%d<​sub>​max</​sub>​)^2;​
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-| <​sub>​{{Technical_Reference%20V4-1_files:​image195.gif?​368x25}}</​sub>​ | (12‑2) |+| <​sub>​{{techref_files:​image195.gif?​368x25}}</​sub>​ | (12‑2) |
  
 where where
  
-<​sub>​{{Technical_Reference%20V4-1_files:​image197.gif?​119x27}}</​sub><​sub>​{{Technical_Reference%20V4-1_files:​image199.gif?​89x27}}</​sub><​sub>​{{Technical_Reference%20V4-1_files:​image201.gif?​59x25}}</​sub><​sub>​{{Technical_Reference%20V4-1_files:​image203.gif?​160x25}}</​sub><​sub>​{{Technical_Reference%20V4-1_files:​image205.gif?​93x24}}</​sub><​sub>​{{Technical_Reference%20V4-1_files:​image207.gif?​92x24}}</​sub>​====== 13       Batch mode operation – TC.EXE ======+<​sub>​{{techref_files:​image197.gif?​119x27}}</​sub><​sub>​{{techref_files:​image199.gif?​89x27}}</​sub><​sub>​{{techref_files:​image201.gif?​59x25}}</​sub><​sub>​{{techref_files:​image203.gif?​160x25}}</​sub><​sub>​{{techref_files:​image205.gif?​93x24}}</​sub><​sub>​{{techref_files:​image207.gif?​92x24}}</​sub>​====== 13       Batch mode operation – TC.EXE ======
  
 The command line program tc.exe provides for batch mode operation. Running tc.exe without arguments displays help information. Running an INP file is as follows: The command line program tc.exe provides for batch mode operation. Running tc.exe without arguments displays help information. Running an INP file is as follows:

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