8.3.13 PBE MASK Command

Syntax

     PBE MASK data-name relop real [ABS] [USING data-name] [SETTO real]
              [RECALL name]
     
                   { PHI   }
                   { RHO   }
     data-name ::= { KAPPA }
                   { EPSX  }
                   { EPSY  }
                   { EPSZ  }
     
               { GT }
               { GE }
     relop ::= { LT }
               { LE }
               { EQ }
               { NE }

Function

The PBE MASK command allows the user to identify or mask values in any of the grids. This is useful for identifying interesting regions prior to plotting, or for gathering statistics about regions of the system. For example, it is possible to mask all regions of the potential that lie within the van der Waals surface, and then calculate statistics on the outer regions.

The options have the following meanings:

Option

Purpose

data-name

The data structure being changed.

relop real

The relop specifies a relational operator for which each array element is compared against the reference number, given by the real, and if the relationship is true, the corresponding array element is changed.

ABS

Absolute values of the reference number and the array elements are used for comparison.

USING data-name

By default, the comparison done by this command are done on the same array as the one being modified. When the USING option is invoked, it specifies the array to be used for comparisons.

SETTO real

Specifies the new value for data elements which satisfy the masking condition. The default is zero.

RECALL name

Normally, the reference data structure is the same as the one being masked. The RECALL option specifies the name of the another pbe_info data structure to be used for the reference array.

The following commands illustrates setting the potential to zero for all points within and including the Stern layer. Note that this command depends on the ionic strength being positive.

     PBE MASK PHI EQ 0.0 USING KAPPA