10.    Free Variables (FVAR)

There may come a time when you have an ion or molecule with high thermal parameters that you suspect may be partially occupied.  Instead of just setting the occupancy to 0.5, you may want to try refining atomic occupancies for this species.  To refine occupancies as a group, use a free variable to restrain the occupancies of all the atoms to the same value.

FVAR   0.48245   0.60406   0.52260   1.03682   0.51762   0.67880   0.59571
FVAR   0.75427   0.64950   0.50344   0.53847
 

The free variables listed above would be referenced in the .ins file based on their position in the FVAR line.  Thus, there are 11 free variables listed above.

The first free variable is the overall scale factor, and as such is not a user defined FVAR.  So, free variables that you will use to define group occupancies, group thermal parameters, etc., are defined beginning with the second FVAR.

In the .ins file used in this example, the third free variable has been used to define the occupancies of a sulfate ion:

RESI  252   SO4
S     5   0.396840   0.561228   0.099061   31.00000   0.09976    0.13994 =
         0.09484    0.02221    0.02566    0.07635
O1    4   0.416268   0.562718   0.108558   31.00000   0.12158    0.15105 =
         0.15293    0.01396   -0.01394    0.09241
O2    4   0.397212   0.582708   0.103067   31.00000   0.21965    0.14678 =
         0.20833   -0.03390   -0.12033    0.13435
O3    4   0.401033   0.565731   0.080906   31.00000   0.12720    0.21287 =
         0.11832    0.04303    0.01685    0.06167
O4    4   0.376779   0.540346   0.102920   31.00000   0.11734    0.12538 =
         0.13833    0.02512    0.07834    0.07414
 

Note that to reference the free variable, the occupancy is written as 31.00000.  This means, in SHELX lingo, that the occupancy is equal to the third free variable multiplied by 1.00000 (a value of 30.50000 would mean that the occupancy would be equal to the third free variable mutliplied by 0.50000).

Notice that the fourth free variable has a value greater than unity.  Since this was used to refine an occupancy, this would mean that the species that it referred to was fully occupied.
 

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