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bond_valence_restraints [2011/11/24 13:36]
ivana created
bond_valence_restraints [2020/07/16 11:29] (current)
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 ====== Bond Valence Restraints ====== ====== Bond Valence Restraints ======
  
-It's often useful to restrain bond valence sums rather than distances and angles. ​ See e.g. user meeting notes from Bad Herrenalb or original literature on La2Mo2O9.+It's often useful to restrain bond valence sums rather than distances and angles. ​ See e.g. Ivana Evans' ​user meeting notes from Bad Herrenalb or original literature on La2Mo2O9.
  
 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)); ​ 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;​ prm  W1_1_num =  W1_1_val;:​6.09633`+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;​ 
 +prm  W1_1_num =  W1_1_val;:​6.09633`
  
-'this is restraint for an O site 
  
-atomic_interaction ​ O1_1_val = (Exp((1.900-R)/​0.37)); ​ ai_radius 3.5 ai_sites_1 ​ O1_1 ai_sites_2 "W2_3 W1_1" penalty = val_weight ( O1_1_val-2)^2;​ prm  O1_1_num =  O1_1_val;:​2.02801`+'this is valence penalty for an O site 
 +
 +atomic_interaction ​ O1_1_val = (Exp((1.900-R)/​0.37));  ​ 
 +ai_radius 3.5 ai_sites_1 ​ O1_1 ai_sites_2 "W2_3 W1_1" penalty = val_weight ( O1_1_val-2)^2; ​ 
 +prm  O1_1_num =  O1_1_val;:​2.02801`
 </​code>​ </​code>​
  

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