FRAGMENT: A Collection of Scripts to Obtain Magnetic Exchange, Electron Transfer and Orbital Energy on Polyoxometalates

Abstract

A new computer program called FRAGMENT has been designed to help MOLCAS users
in the task of preparing the input files for spectroscopic calculations on embedded fragments of
magnetic molecules. FRAGMENT is built as a collection of bash shell scripts (FRAGMENTador
and FRAGMENTazor) and can execute the following operations: (a) read atomic coordinate files
of complex molecules and largely automate the preparation of a large variety of molecular
fragments; (b) perform Bond Valence Sum calculations, (c) prepare POV-Ray files for raytracing
representations of said fragments and (d) extract all in-fragment angles and distances of
possible magnetostructural meaning; (e) manage different programs (seward, scf, rasscf) of the
MOLCAS chain, including (f) preparing the input for the sewardprogram, (g) checking the
convergence of scfand rasscfprograms, (h) automatically preparing inputs with different spin
multiplicity for calculating magnetic exchange, electron transfer and orbital energy differences
and (i) calculate said parameters from the results. FRAGMENT has already been applied for the
investigation of a mixed-valence polyoxometalate with interest in molecular magnetism and
quantum computing.