# Differences

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 manual_part_3 [2009/08/26 15:02]clare manual_part_3 [2009/08/27 09:54]clare Both sides previous revision Previous revision 2009/08/27 09:54 clare 2009/08/26 15:02 clare 2009/08/26 14:59 clare created 2009/08/27 09:54 clare 2009/08/26 15:02 clare 2009/08/26 14:59 clare created Line 1: Line 1: + ====== 11       Charge-flipping ====== ====== 11       Charge-flipping ====== Line 103: Line 104: 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}}​ | (11‑1) | + | <​sub>​{{techref_files:​image171.gif?​175x48}}​ | (11‑1) | where //d// corresponds to the electron density threshold. where //d// corresponds to the electron density threshold. Line 482: Line 483: 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}}//​flip_regime_2//​ is typically ramped from 1 to 0. + <​sub>​{{techref_files:​image173.gif?​264x28}}//​flip_regime_2//​ is typically ramped from 1 to 0. **[//​flip_regime_3//​ !E]** **[//​flip_regime_3//​ !E]** Line 488: Line 489: 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}}​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}}​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]** Line 675: Line 676: 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}}​ + '​symmetry error' = <​sub>​{{techref_files:​image177.gif?​127x29}}​ where the summation is over all of the electron density grid points. where the summation is over all of the electron density grid points. Line 701: Line 702: //​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>​{{Technical_Reference%20V4-1_files:​image181.gif?​76x25}}{{Technical_Reference%20V4-1_files:​image183.gif?​48x24}}​ <​sub>​{{Technical_Reference%20V4-1_files:​image185.gif?​215x36}}​  <​sub>​{{Technical_Reference%20V4-1_files:​image187.gif?​219x36}}​ <​sub>​{{Technical_Reference%20V4-1_files:​image189.gif?​113x27}},​ <​sub>​{{Technical_Reference%20V4-1_files:​image191.gif?​100x31}}​ | (1) | + | <​sub>​{{techref_files:​image179.gif?​210x25}}​ <​sub>​{{techref_files:​image181.gif?​76x25}}{{techref_files:​image183.gif?​48x24}}​ <​sub>​{{techref_files:​image185.gif?​215x36}}​  <​sub>​{{techref_files:​image187.gif?​219x36}}​ <​sub>​{{techref_files:​image189.gif?​113x27}},​ <​sub>​{{techref_files:​image191.gif?​100x31}}​ | (1) | **[//​user_threshold//​ !E]** **[//​user_threshold//​ !E]** Line 722: Line 723: view_cloud = Mod(Cycle_Iter,​ 10) == 0; view_cloud = Mod(Cycle_Iter,​ 10) == 0; + + ====== 12       Indexing ====== ====== 12       Indexing ====== Line 947: Line 950: Defines //​X<​sub>​hh//​ in the reciprocal lattice equation: Defines //​X<​sub>​hh//​ in the reciprocal lattice equation: - <​sub>​{{Technical_Reference%20V4-1_files:​image193.gif?​319x50}}​In a triclinic lattice the highest d-spacing can probably be indexed as 100 or 200 etc. Thus + <​sub>​{{techref_files:​image193.gif?​319x50}}​In a triclinic lattice the highest d-spacing can probably be indexed as 100 or 200 etc. Thus index_x0 = 1%%/​(%%d<​sub>​max​)^2;​ index_x0 = 1%%/​(%%d<​sub>​max​)^2;​ Line 1181: Line 1184: - | <​sub>​{{Technical_Reference%20V4-1_files:​image195.gif?​368x25}}​ | (12‑2) | + | <​sub>​{{techref_files:​image195.gif?​368x25}}​ | (12‑2) | where where - <​sub>​{{Technical_Reference%20V4-1_files:​image197.gif?​119x27}}<​sub>​{{Technical_Reference%20V4-1_files:​image199.gif?​89x27}}<​sub>​{{Technical_Reference%20V4-1_files:​image201.gif?​59x25}}<​sub>​{{Technical_Reference%20V4-1_files:​image203.gif?​160x25}}<​sub>​{{Technical_Reference%20V4-1_files:​image205.gif?​93x24}}<​sub>​{{Technical_Reference%20V4-1_files:​image207.gif?​92x24}}​====== 13       Batch mode operation – TC.EXE ====== + <​sub>​{{techref_files:​image197.gif?​119x27}}<​sub>​{{techref_files:​image199.gif?​89x27}}<​sub>​{{techref_files:​image201.gif?​59x25}}<​sub>​{{techref_files:​image203.gif?​160x25}}<​sub>​{{techref_files:​image205.gif?​93x24}}<​sub>​{{techref_files:​image207.gif?​92x24}}​====== 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: