NoMolRec

[-]nomolrec

Setting this logical keyword avoids recognition of independent molecules (if any) in the data input deck.

The geometry section of any IDF may comprise a single molecule, a dimer or an ensemble of molecules. For periodic systems, it describes the asymmetric unit, which in turn may comprise one or more molecules and/or fractions of them.

PAMoC figures out how many Independent Set of Bonded Atoms (ISBAs) are contained in a given group of atoms and then orders the atoms by ISBAs. An ISBA can be an ion, a molecule, as well as a fraction of an ion or a molecule.

In the case of periodic systems, this procedure is repeated after generation of the unit cell and the whole crystal, so that reconstruction of entire molecules from their fragments in the asymmetric unit is accomplished.

Afterwards, all calculations will follow this description of the whole system through its constituent elements. For instance, molecular moments will be calculated for all the independent molecules as well as for the whole system. Similarly, interaction energies among independent molecules will also be calculated.

The only effect of setting option nomolrec is to ignore the description of the whole system through its constituent elements.

An obvious reason is to simplify data output, if you are not interested in the constituent parts of your system.

Actually, the main usage of nomolrec is related to the calculation of crystal cohesion energies. Let's consider an asymmetric unit containing the dimer AB. We are interested in the mean crystal cohesion energy of the monomers A and B, which is given by:

where E_cohesion,A, E_cohesion,B, and E_cohesion,AB are the crystal cohesion energies of monomer A, monomer B and dimer AB, respectively, and E_AB is the dissociation energy of dimer AB into monomers A and B. Now, E_cohesion,AB is calculated by PAMoC when nomolrec is set, whereas the other three energy terms are calculated when nomolrec is not set.

When nomolrec is set, PAMoc prints the message:

 *** WARNING - The asymmetric unit contains 2 independent sets of bonded atoms.
               Still they will be considered as a whole, due to option NoMolRec being set.

  1) Set nr. 1 contains 24 atoms (  1 through 24)
  2) Set nr. 2 contains 24 atoms ( 25 through 48)

(frg|fra|frag): this option gives the way to specify molecular fragments for which properties, like moments and interaction energies, will be calculated, in addition to the properties of the molecule itself. In a sense, it has an effect opposite to that of nomolrec.