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bond_valence_restraints [2011/11/24 13:36]
ivana
bond_valence_restraints [2016/10/27 08:36]
johnsoevans
Line 5: Line 5:
 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 restraint for a W site
 +'
 +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 '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`+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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