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bond_valence_restraints [2011/12/01 23:52]
rowlesmr Fixed some topas code formatting and added some extra comment markers to fix auto code colouring
bond_valence_restraints [2016/10/27 08:38]
johnsoevans
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 You can do this in Topas using the atomic_interaction lines and associated penalties below. ​ In the example below 1.900 is the Rij value for W-O.  I've listed the specific sites that each atom bonds to in the structure, though you could use e.g. O*. You can do this in Topas using the atomic_interaction lines and associated penalties below. ​ In the example below 1.900 is the Rij value for W-O.  I've listed the specific sites that each atom bonds to in the structure, though you could use e.g. O*.
  
-This example was in P1 with Z=1.  If Z is not equal to one then you may find that the valence sum (reported at the end of the line) is wrong. ​ You'd then need to divide the value calculated by Z (e.g. divide by 2/4/8).+This example was in P1 with Z=1.  If Z is not equal to one then you may find that the valence sum (reported at the end of the line) is wrong. ​ You'd then need to divide the value calculated by Z (e.g. divide by 2/​4/​8). ​ Be very careful about this!
  
 <code topas> <code topas>
-'this is restraint ​for a W site+'this is valence penalty ​for a W site
 ' '
 +prm !val_weight 1.0 'this weights the valence penalties relative to other penalties
 +
 atomic_interaction ​ W1_1_val = (Exp((1.900-R)/​0.37));  ​ atomic_interaction ​ W1_1_val = (Exp((1.900-R)/​0.37));  ​
 ai_radius 3.5 ai_sites_1 ​ W1_1 ai_sites_2 "O3_1 O2_2 O1_1 O6_2 O3_2 O5_1" penalty = val_weight ( W1_1_val-6)^2;​ ai_radius 3.5 ai_sites_1 ​ W1_1 ai_sites_2 "O3_1 O2_2 O1_1 O6_2 O3_2 O5_1" penalty = val_weight ( W1_1_val-6)^2;​
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-'this is restraint ​for an O site+'this is valence penalty ​for an O site
 ' '
 atomic_interaction ​ O1_1_val = (Exp((1.900-R)/​0.37));  ​ atomic_interaction ​ O1_1_val = (Exp((1.900-R)/​0.37));  ​

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