# Differences

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 bond_valence_restraints [2011/11/24 13:36]ivana bond_valence_restraints [2020/07/16 11:29] (current) Both sides previous revision Previous revision 2016/10/27 08:38 johnsoevans 2016/10/27 08:36 johnsoevans 2011/12/01 23:52 rowlesmr Fixed some topas code formatting and added some extra comment markers to fix auto code colouring2011/11/24 13:36 ivana 2011/11/24 13:36 ivana created Next revision Previous revision 2016/10/27 08:38 johnsoevans 2016/10/27 08:36 johnsoevans 2011/12/01 23:52 rowlesmr Fixed some topas code formatting and added some extra comment markers to fix auto code colouring2011/11/24 13:36 ivana 2011/11/24 13:36 ivana created 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! - '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`