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<TITLE>23. Hybrid Calculations with ONIOM</TITLE>
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<B> Next:</B> <A NAME="tex2html1457"
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HREF="node26.html">24. Hessians</A>
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<B> Previous:</B> <A NAME="tex2html1447"
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HREF="node24.html">22. Constraints for Geometry</A>
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  <B> <A NAME="tex2html1455"
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HREF="node2.html">Contents</A></B>
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<!--Table of Child-Links-->
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<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
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<UL>
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<LI><A NAME="tex2html1458"
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HREF="node25.html#SECTION002510000000000000000">23.1 Real, model and intermediate geometries</A>
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<UL>
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<LI><A NAME="tex2html1459"
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HREF="node25.html#SECTION002511000000000000000">23.1.1 Link atoms</A>
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<LI><A NAME="tex2html1460"
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HREF="node25.html#SECTION002512000000000000000">23.1.2 Numbering of the link atoms</A>
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</UL>
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<BR>
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<LI><A NAME="tex2html1461"
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HREF="node25.html#SECTION002520000000000000000">23.2 High, medium and low theories</A>
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<UL>
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<LI><A NAME="tex2html1462"
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HREF="node25.html#SECTION002521000000000000000">23.2.1 Basis specification</A>
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<LI><A NAME="tex2html1463"
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HREF="node25.html#SECTION002522000000000000000">23.2.2 Effective core potentials</A>
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<LI><A NAME="tex2html1464"
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HREF="node25.html#SECTION002523000000000000000">23.2.3 General input strings</A>
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</UL>
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<BR>
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<LI><A NAME="tex2html1465"
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HREF="node25.html#SECTION002530000000000000000">23.3 Use of symmetry</A>
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<LI><A NAME="tex2html1466"
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HREF="node25.html#SECTION002540000000000000000">23.4 Molecular orbital files</A>
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<LI><A NAME="tex2html1467"
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HREF="node25.html#SECTION002550000000000000000">23.5 Restarting</A>
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<LI><A NAME="tex2html1468"
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HREF="node25.html#SECTION002560000000000000000">23.6 Examples</A>
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<UL>
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<LI><A NAME="tex2html1469"
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HREF="node25.html#SECTION002561000000000000000">23.6.1 Hydrocarbon bond energy</A>
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<LI><A NAME="tex2html1470"
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HREF="node25.html#SECTION002562000000000000000">23.6.2 Optimization and frequencies</A>
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<LI><A NAME="tex2html1471"
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HREF="node25.html#SECTION002563000000000000000">23.6.3 A three-layer example</A>
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<LI><A NAME="tex2html1472"
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HREF="node25.html#SECTION002564000000000000000">23.6.4 DFT with and without charge fitting</A>
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</UL></UL>
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<!--End of Table of Child-Links-->
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<HR>
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<H1><A NAME="SECTION002500000000000000000">
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23. Hybrid Calculations with ONIOM</A>
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</H1>
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<A NAME="sec:oniom"></A>
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<P>
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ONIOM is the hybrid method of Morokuma and co-workers that enables
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different levels of theory to be applied to different parts of a
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molecule/system and combined to produce a consistent energy
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expression. The objective is to perform a high-level calculation on
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just a small part of the system and to include the effects of the
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remainder at lower levels of theory, with the end result being of
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similar accuracy to a high-level calculation on the full system.
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<P>
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<OL>
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<LI>M. Svensson, S. Humbel, R.D.J. Froese, T. Mastubara, S. Sieber, and
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K. Morokuma, J. Phys. Chem., 100, 19357 (1996).
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</LI>
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<LI>S. Dapprich, I. Komaromi, K.S. Byun, K. Morokuma, and M.J. Frisch,
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J. Mol. Struct. (Theochem), 461-462, 1 (1999).
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</LI>
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<LI>R.D.J. Froese and K. Morokuma in ``Encylopedia of Computational Chemistry,''
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volume 2, pp.1244-1257, (ed. P. von Rague Schleyer, John Wiley and Sons,
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Chichester, Sussex, 1998).
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</LI>
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</OL>
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<P>
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The NWChem ONIOM module implements two- and three-layer ONIOM models
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for use in energy, gradient, geometry optimization, and vibrational
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frequency calculations with any of the pure quantum mechanical methods
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within NWChem. At the present time, it is not possible to perform
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ONIOM calculations with either solvation models or classical force
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fields. Nor is it yet possible to compute properties except as
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derivatives of the total energy.
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<P>
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Using the terminology of Morokuma et al., the full molecular geometry
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including all atoms is referred to as the ``real'' geometry and it is
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treated using a ``low''-level of theory. A subset of these atoms
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(referred to as the ``model'' geometry) are treated using both the
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``low''-level and a ``high''-level of theory. A three-layer model
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also introduces an ``intermediate'' model geometry and a ``medium''
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level of theory.
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<P>
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The two-layer model requires a high and low level of theory and a
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real and model molecular geometry. The energy at the high-level of
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theory for the real geometry is estimated as
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<PRE>
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E(High,Real) = E(Low,Real) + [E(High,Model) - E(Low,Model)].
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</PRE>
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The three-layer model requires high, medium and low levels of theory,
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and real, intermediate and model geometries and the corresponding
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energy estimate is
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<PRE>
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E(High,Real) = E(Low,Real) + [E(High,Model) - E(Medium,Model)]
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+ [E(Medium,Inter) - E(Low,Inter)].
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</PRE>
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<P>
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When does ONIOM work well? The approximation for a two-layer model
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will be good if
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<UL>
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<LI>the model system includes the interactions that dominate the
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energy difference being computed and the high-level of theory
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describes these to the required precision, and
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</LI>
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<LI>the interactions between the model and the rest of the real system
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(substitution effects) are described to sufficient accuracy at the
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lower level of theory.
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</LI>
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</UL>
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ONIOM is used to compute energy differences and the absolute energies
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are not all that meaningful even though they are well defined. Due to
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cancellation of errors, ONIOM actually works better than you might
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expect, but a poorly designed calculation can yield very bad results.
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Please read and heed the caution at the end of the article by Dapprich
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et al.
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<P>
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The input options are as follows
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<PRE>
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ONIOM
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HIGH <string theory> [basis <string basis default "ao basis">] \
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[ecp <string ecp>] [input <string input>]
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[MEDIUM <string theory> [basis <string basis default "ao basis">] \
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[ecp <string ecp>] [input <string input>]]
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LOW <string theory> [basis <string basis default "ao basis">] \
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[ecp <string ecp>] [input <string input>]
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MODEL <integer natoms> [charge <double charge>] \
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[<integer i1 j1> <real g1> [<string tag1>] ...]
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[INTER <integer natoms> [charge <double charge>] \
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[<integer i1 j1> <real g1> [<string tag1>] ...]]
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[VECTORS [low-real <string mofile>] [low-model <string mofile>] \
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[high-model <string mofile>] [medium-model <string mofile]\
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[medium-inter <string mofile>] [low-inter <string mofile>]]
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[PRINT ...]
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[NOPRINT ...]
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END
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</PRE>
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which are described in detail below.
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<P>
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<EM>For better validation of user input, the <code>HIGH</code>,
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<code>LOW</code> and <code>MODEL</code> directives must always be specified. If
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the one of the <code>MEDIUM</code> or <code>INTER</code> directives are specified,
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then so must the other.</EM>
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<P>
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<H1><A NAME="SECTION002510000000000000000">
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23.1 Real, model and intermediate geometries</A>
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</H1>
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<P>
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The geometry and total charge of the full or real system should be
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specified as normal using the geometry directive (see Section
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<A HREF="node8.html#sec:geom">6</A>). If <IMG
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WIDTH="52" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
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SRC="img166.gif"
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ALT="$N_{model}$"> of the atoms are to be included in
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the model system, then these should be specified first in the
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geometry. Similarly, in a three-layer calculation, if there are
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<IMG
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WIDTH="47" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
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SRC="img167.gif"
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ALT="$N_{inter}$"> atoms to be included in the intermediate system, then
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these should also be arranged together at the beginning of the
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geometry. The implict assumption is that the model system is a subset
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of the intermediate system which is a subset of the real system. The
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number of atoms to be included in the model and intemediate systems
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are specified using the <code>MODEL</code> and <code>INTER</code> directives.
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Optionally, the total charge of the model and intermediate systems may
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be adjusted. The default is that all three systems have the same
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total charge.
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<P>
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|
Example 1. A two-layer calculation on <IMG
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WIDTH="75" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
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SRC="img168.gif"
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ALT="$K^{+}(H_2O)$"> taking the
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potassium ion as the model system. Note that no bonds are broken so
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no link atoms are introduced. The real geometry would be specified
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with potassium (the model) first.
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<PRE>
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geometry autosym
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K 0 0.00 1.37
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O 0 0.00 -1.07
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H 0 -0.76 -1.68
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H 0 0.76 -1.68
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end
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</PRE>
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and the following directive in the ONIOM input block indicates that
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one atom (implicitly the first in the geometry) is in the model system
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<PRE>
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model 1
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</PRE>
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<P>
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<H2><A NAME="SECTION002511000000000000000">
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23.1.1 Link atoms</A>
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</H2>
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Link atoms for bonds spanning two regions are automatically generated
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from the bond information. The additional parameters on the
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<code>MODEL</code> and <code>INTER</code> directives describe the broken bonds
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including scale factors for placement of the link atom
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and, optionally, the type of link atom. The type of link atom
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defaults to hydrogen, but any type may be specified (actually here you
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are specifying a geometry tag which is used to associate a geometrical
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center with an atom type and basis sets, etc.. See section
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<A HREF="node8.html#sec:cart">6.3</A>).
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For each broken bond specify the numbers of the two atoms (i and j),
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the scale factor (g) and optionally the tag of the link atom. Link
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atoms are placed along the vector connecting the the first to the
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second atom of the bond according to the equation
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<BR><P></P>
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<DIV>
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<!-- MATH
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\begin{displaymath}
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\underline{R}_{link} = (1-g)\underline{R}_{1} + g*\underline{R}_{2}
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\end{displaymath}
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-->
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<IMG
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WIDTH="186" HEIGHT="62" BORDER="0"
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SRC="img169.gif"
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ALT="\begin{displaymath}
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\underline{R}_{link} = (1-g)\underline{R}_{1} + g*\underline{R}_{2}
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\end{displaymath}">
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</DIV>
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<BR CLEAR="ALL">
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<P></P>
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where <IMG
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WIDTH="12" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
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SRC="img170.gif"
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ALT="$g$"> is the scale factor. If the scale factor is one, then the
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link atom is placed where the second atom was. More usually, the
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scale factor is less than one, in which case the link atom is placed
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between the original two atoms. The scale factor should be chosen so
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that the link atom (usually hydrogen) is placed near its equilibrium
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bond length from the model atom. E.g., when breaking a single
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carbon-carbon bond (typical length 1.528 Angstrøms) using a hydrogen
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link atom we will want a carbon-hydrogen bond length of about 1.084
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Angstrøms, so the scale factor should be chosen as <!-- MATH
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$1.084/1.528
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\approx 0.709$
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-->
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<IMG
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WIDTH="142" HEIGHT="31" ALIGN="MIDDLE" BORDER="0"
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SRC="img171.gif"
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ALT="$1.084/1.528
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\approx 0.709$">.
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<P>
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Example 2. A calculation on acetaldehyde (<IMG
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WIDTH="96" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
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SRC="img172.gif"
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ALT="$H_3C-CHO$">) using aldehyde
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(<IMG
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WIDTH="78" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
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SRC="img173.gif"
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ALT="$H-CHO$">) as the model system. The covalent bond between the two
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carbon atoms is broken and a link atom must be introduced to replace
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the methyl group. The link atom is automatically generated -- all
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you need to do is specify the atoms in the model system that are also
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in the real system (here <IMG
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WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
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SRC="img174.gif"
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ALT="$CHO$">) and the broken bonds. Here is the
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geometry of acetaldehyde with the <IMG
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WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
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SRC="img174.gif"
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ALT="$CHO$"> of aldehyde first
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<PRE>
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geometry
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C -0.383 0.288 0.021
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H -1.425 0.381 0.376
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O 0.259 1.263 -0.321
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H 0.115 -1.570 1.007
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H -0.465 -1.768 -0.642
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H 1.176 -1.171 -0.352
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C 0.152 -1.150 0.005
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end
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</PRE>
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There are three atoms (the first three) of the real geometry included
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in the model geometry, and we are breaking the bond between atoms 1
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and 7, replacing atom 7 with a hydrogen link atom. This is all
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accomplished by the directive
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<PRE>
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model 3 1 7 0.709 H
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</PRE>
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Since the default link atom is hydrogen there is actually no need to
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specify the ``H''.
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|
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<P>
|
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See also Section <A HREF="node25.html#sec:oniomeg3">23.6.3</A> for a more complex example.
|
|
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<P>
|
|
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<H2><A NAME="SECTION002512000000000000000">
|
|
23.1.2 Numbering of the link atoms</A>
|
|
</H2>
|
|
|
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<P>
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The link atoms are appended to the atoms of the model or intermediate
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systems in the order that the broken bonds are specified in the input.
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This is of importance only if manually constructing an initial guess.
|
|
|
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<P>
|
|
|
|
<H1><A NAME="SECTION002520000000000000000">
|
|
23.2 High, medium and low theories</A>
|
|
</H1>
|
|
|
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<P>
|
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The two-layer model requires both the high-level and low-level
|
|
theories be specified. The three-layer model also requires the
|
|
medium-level theory. Each of these includes a theory (such as SCF,
|
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MP2, DFT, CCSD, CCSD(T), etc.), an optional basis set, an optional ECP,
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and an optional string containing general NWChem input.
|
|
|
|
<P>
|
|
|
|
<H2><A NAME="SECTION002521000000000000000">
|
|
23.2.1 Basis specification</A>
|
|
</H2>
|
|
The basis name on the theory directive (high, medium, or low) is that
|
|
specified on a basis set directive (see Section <A HREF="node9.html#sec:basis">7</A>) and
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<EM>not</EM> the name of a standard basis in the library. If not
|
|
specified, the basis set for the high-level theory defaults to the
|
|
standard <code>"ao basis"</code>. That for the medium level defaults to the
|
|
high-level basis, and the low-level basis defaults to the medium-level
|
|
basis. Other wavefunction parameters are obtained from the standard
|
|
wavefunction input blocks. See <A HREF="node25.html#sec:oniomeg2">23.6.2</A> for an example.
|
|
|
|
<P>
|
|
|
|
<H2><A NAME="SECTION002522000000000000000">
|
|
23.2.2 Effective core potentials</A>
|
|
</H2>
|
|
|
|
<P>
|
|
If an effective core potential is specified in the usual fashion (see
|
|
Section <A HREF="node10.html#sec:ecp">8</A>) outside of the ONIOM input then this will be
|
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used in all calculations. If an alternative ECP name (the name
|
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specified on the ECP directive in the same manner as done for basis
|
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sets) is specified on one of the theory directives, then this ECP will
|
|
be used in preference for that level of theory. See Section
|
|
<A HREF="node25.html#sec:oniomeg2">23.6.2</A> for sample input.
|
|
|
|
<P>
|
|
|
|
<H2><A NAME="SECTION002523000000000000000">
|
|
23.2.3 General input strings</A>
|
|
</H2>
|
|
|
|
<P>
|
|
For many purposes, the ability to specify the theory, basis and
|
|
effective core potential is adequate. All of the options for each
|
|
theory are determined from their independent input blocks. However,
|
|
if the same theory (e.g., DFT) is to be used with different options
|
|
for the ONIOM theoretical models, then the general input strings must
|
|
be used. These strings are processed as NWChem input each time the
|
|
theoretical model is invoked. The strings may contain any NWChem
|
|
input, except for options pertaining to ONIOM and the task directive.
|
|
The intent that the strings be used just to control the options
|
|
pertaining to the theory being used.
|
|
|
|
<P>
|
|
A word of caution. Be sure to check that the options are producing
|
|
the desired results. Since the NWChem database is persistent and the
|
|
ONIOM calculations happen in an undefined order, the input strings
|
|
should fully define the calculation you wish to have happen.
|
|
|
|
<P>
|
|
For instance, if the high model is DFT/B3LYP/6-311g** and the
|
|
low model is DFT/LDA/3-21g, the ONIOM input might look like this
|
|
<PRE>
|
|
oniom
|
|
model 3
|
|
low dft basis 3-21g input "dft\; xc\; end"
|
|
high dft basis 6-311g** input "dft\; xc b3lyp\; end"
|
|
end
|
|
</PRE>
|
|
The empty <code>XC</code> directive restores the default LDA
|
|
exchange-correlation option (see Section <A HREF="node13.html#sec:xc">11.3</A>). Note that
|
|
semi-colons and other quotation marks inside the input string must be
|
|
preceded by a backslash to avoid special interpretation.
|
|
|
|
<P>
|
|
See Section <A HREF="node25.html#sec:oniomeg4">23.6.4</A> for another example.
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION002530000000000000000">
|
|
23.3 Use of symmetry</A>
|
|
</H1>
|
|
|
|
<P>
|
|
Symmetry should work just fine as long as the model and intermediate
|
|
regions respect the symmetry -- i.e., symmetry equivalent atoms need
|
|
to be treated equivalently. If symmetry equivalent atoms must be
|
|
treated in separate regions then the symmetry must be lowered (or
|
|
completely switched off).
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION002540000000000000000">
|
|
23.4 Molecular orbital files</A>
|
|
</H1>
|
|
|
|
<P>
|
|
The <code>VECTORS</code> directive in the ONIOM block is different to that
|
|
elsewhere in NWChem. For each of the necessary combinations of theory
|
|
and geometry you can specify a different file for the molecular
|
|
orbitals. By default each combination will store the MO vectors in
|
|
the permanent directory using a file name created by appending to the
|
|
name of the calculation the following string
|
|
|
|
<UL>
|
|
<LI>low-real -- <code>".lrmos"</code>
|
|
</LI>
|
|
<LI>low-inter -- <code>".limos"</code>
|
|
</LI>
|
|
<LI>low-model -- <code>".lmmos"</code>
|
|
</LI>
|
|
<LI>medium-inter -- <code>".mimos"</code>
|
|
</LI>
|
|
<LI>medium-model -- <code>".mmmos"</code>
|
|
</LI>
|
|
<LI>high-model -- <code>".hmmos"</code>
|
|
</LI>
|
|
</UL>
|
|
Each calculation will utilize the appropriate vectors which is more
|
|
efficient during geometry optimizations and frequency calculations,
|
|
and is also useful for the initial calculation. In the absence of
|
|
existing MO vectors files, the default atomic guess is used (see
|
|
Section <A HREF="node12.html#sec:vectors">10.5</A>).
|
|
|
|
<P>
|
|
If special measures must be taken to converge the initial SCF, DFT or
|
|
MCSCF calculation for one or more of the systems, then initial vectors
|
|
may be saved in a file with the default name, or another name may be
|
|
specified using the <code>VECTORS</code> directive. Note that subsequent
|
|
vectors (e.g., from a geometry optimization) will be written back to
|
|
this file, so take a copy if you wish to preserve it.
|
|
To generate the initial guess for the model or intermediate systems
|
|
it is necessary to generate the geometries which is most readily
|
|
done, if there are link atoms, by just running NWChem on the
|
|
input for the ONIOM calculation on your workstation. It will
|
|
print these geometries before starting any calculations which
|
|
you can then terminate.
|
|
|
|
<P>
|
|
E.g., in a calculation on Fe(III) surrounded by some ligands, it is
|
|
hard to converge the full (real) system from the atomic guess so as to
|
|
obtain a <IMG
|
|
WIDTH="20" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img94.gif"
|
|
ALT="$d^5$"> configuration for the iron atom since the <IMG
|
|
WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img64.gif"
|
|
ALT="$d$"> orbitals
|
|
are often nominally lower in energy than some of the ligand orbitals.
|
|
The most effective mechanism is to converge the isolated Fe(III) and
|
|
then to use the fragment guess (see Section <A HREF="node12.html#sec:fragguess">10.5.1</A>) as a
|
|
starting guess for the real system. The resulting converged molecular
|
|
orbitals can be saved either with the default name (as described above
|
|
in this section), in which case no additional input is necessary. If
|
|
an alternative name is desired, then the <code>VECTORS</code> directive may
|
|
be used as follows
|
|
<PRE>
|
|
vectors low-real /u/rjh/jobs/fe_ether_water.mos
|
|
</PRE>
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION002550000000000000000">
|
|
23.5 Restarting</A>
|
|
</H1>
|
|
|
|
<P>
|
|
Restart of ONIOM calculations does not currently work as smoothly as
|
|
we would like. For geometry optimizations that terminated gracefully
|
|
by running out of iterations, the restart will work as normal.
|
|
Otherwise, specify in the input of the restart job the last geometry
|
|
of the optimization. The Hessian information will be reused and the
|
|
calculation should proceed losing at most the cost of one ONIOM
|
|
gradient evaluation. For energy or frequency calculations, restart
|
|
may not currently be possible.
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION002560000000000000000">
|
|
23.6 Examples</A>
|
|
</H1>
|
|
|
|
<P>
|
|
|
|
<H2><A NAME="SECTION002561000000000000000"></A>
|
|
<A NAME="sec:oniomeg1"></A>
|
|
<BR>
|
|
23.6.1 Hydrocarbon bond energy
|
|
</H2>
|
|
|
|
<P>
|
|
A simple two-layer model changing just the wavefunction with one
|
|
link atom.
|
|
|
|
<P>
|
|
This reproduces the two-layer ONIOM (MP2:HF) result from Dapprich et
|
|
al. for the reaction <!-- MATH
|
|
$R-CH_3 = R-CH_2 + H$
|
|
-->
|
|
<IMG
|
|
WIDTH="188" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img175.gif"
|
|
ALT="$R-CH_3 = R-CH_2 + H$"> with <IMG
|
|
WIDTH="70" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img176.gif"
|
|
ALT="$R=CH_3$"> using <IMG
|
|
WIDTH="37" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img177.gif"
|
|
ALT="$CH_4$">
|
|
as the model . The geometries of <IMG
|
|
WIDTH="69" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img178.gif"
|
|
ALT="$R-CH_3$"> and <IMG
|
|
WIDTH="69" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img179.gif"
|
|
ALT="$R-CH_2$"> are optimized
|
|
at the DFT-B3LYP/6-311++G** level of theory, and then ONIOM is used to
|
|
compute the binding energy using UMP2 for the model system and HF for
|
|
the real system. The results, including MP2 calculations on the full
|
|
system for comparison, are as given in Table <A HREF="#tab:oniom1">23.1</A>
|
|
|
|
<P>
|
|
<BR><P></P>
|
|
<DIV ALIGN="CENTER"><A NAME="6491"></A>
|
|
<TABLE>
|
|
<CAPTION><STRONG>Table 23.1:</STRONG>
|
|
Energies for ONIOM example 1, hydrocarbon bond energy using MP2:HF two-layer model.</CAPTION>
|
|
<TR><TD>
|
|
<DIV ALIGN="CENTER">
|
|
<TABLE CELLPADDING=3 BORDER="1" ALIGN="CENTER">
|
|
<TR><TD ALIGN="LEFT">Theory</TD>
|
|
<TD ALIGN="CENTER">Me-CH2</TD>
|
|
<TD ALIGN="CENTER">Me-Me</TD>
|
|
<TD ALIGN="CENTER">H</TD>
|
|
<TD ALIGN="CENTER">De(Hartree)</TD>
|
|
<TD ALIGN="CENTER">De(kcal/mol)</TD>
|
|
</TR>
|
|
<TR><TD ALIGN="LEFT">B3LYP</TD>
|
|
<TD ALIGN="CENTER">-79.185062</TD>
|
|
<TD ALIGN="CENTER">-79.856575</TD>
|
|
<TD ALIGN="CENTER">-0.502256</TD>
|
|
<TD ALIGN="CENTER">0.169257</TD>
|
|
<TD ALIGN="CENTER">106.2</TD>
|
|
</TR>
|
|
<TR><TD ALIGN="LEFT">HF</TD>
|
|
<TD ALIGN="CENTER">-78.620141</TD>
|
|
<TD ALIGN="CENTER">-79.251701</TD>
|
|
<TD ALIGN="CENTER">-0.499817</TD>
|
|
<TD ALIGN="CENTER">0.131741</TD>
|
|
<TD ALIGN="CENTER">82.7</TD>
|
|
</TR>
|
|
<TR><TD ALIGN="LEFT">MP2</TD>
|
|
<TD ALIGN="CENTER">-78.904716</TD>
|
|
<TD ALIGN="CENTER">-79.571654</TD>
|
|
<TD ALIGN="CENTER">-0.499817</TD>
|
|
<TD ALIGN="CENTER">0.167120</TD>
|
|
<TD ALIGN="CENTER">104.9</TD>
|
|
</TR>
|
|
<TR><TD ALIGN="LEFT">MP2:HF</TD>
|
|
<TD ALIGN="CENTER">-78.755223</TD>
|
|
<TD ALIGN="CENTER">-79.422559</TD>
|
|
<TD ALIGN="CENTER">-0.499817</TD>
|
|
<TD ALIGN="CENTER">0.167518</TD>
|
|
<TD ALIGN="CENTER">105.1</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
</DIV></TD></TR>
|
|
</TABLE>
|
|
</DIV><P></P>
|
|
<BR>
|
|
|
|
<P>
|
|
The following input first performs a calculation on <IMG
|
|
WIDTH="89" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img180.gif"
|
|
ALT="$CH_3-CH_2$">, and then
|
|
on <IMG
|
|
WIDTH="89" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img181.gif"
|
|
ALT="$CH_3-CH_3$">. Note that in the second calculation we cannot use the
|
|
full symmetry since we are breaking the C-C bond in forming the model
|
|
system (the non-equivalence of the methyl groups is perhaps more
|
|
apparent if we write <IMG
|
|
WIDTH="69" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img178.gif"
|
|
ALT="$R-CH_3$">).
|
|
|
|
<P>
|
|
<PRE>
|
|
start
|
|
|
|
basis spherical
|
|
H library 6-311++G**; C library 6-311++G**
|
|
end
|
|
|
|
title "ONIOM Me-CH2"
|
|
|
|
geometry autosym
|
|
H -0.23429328 1.32498565 0.92634814
|
|
H -0.23429328 1.32498565 -0.92634814
|
|
C -0.13064265 0.77330370 0.00000000
|
|
H -1.01618703 -1.19260361 0.00000000
|
|
H 0.49856072 -1.08196901 -0.88665533
|
|
H 0.49856072 -1.08196901 0.88665533
|
|
C -0.02434414 -0.71063687 0.00000000
|
|
end
|
|
|
|
scf; uhf; doublet; thresh 1e-6; end
|
|
mp2; freeze atomic; end
|
|
|
|
oniom
|
|
high mp2
|
|
low scf
|
|
model 3 3 7 0.724
|
|
end
|
|
|
|
task oniom
|
|
|
|
title "ONIOM Me-Me"
|
|
|
|
geometry # Note cannot use full D3D symmetry here
|
|
H -0.72023641 0.72023641 -1.16373235
|
|
H 0.98386124 0.26362482 -1.16373235
|
|
H -0.26362482 -0.98386124 -1.16373235
|
|
C 0.00000000 0.00000000 -0.76537515
|
|
H 0.72023641 -0.72023641 1.16373235
|
|
H -0.98386124 -0.26362482 1.16373235
|
|
H 0.26362482 0.98386124 1.16373235
|
|
C 0.00000000 0.00000000 0.76537515
|
|
end
|
|
|
|
scf; rhf; singlet; end
|
|
|
|
oniom
|
|
high mp2
|
|
low scf
|
|
model 4 4 8 0.724
|
|
end
|
|
|
|
task oniom
|
|
</PRE>
|
|
|
|
<P>
|
|
|
|
<H2><A NAME="SECTION002562000000000000000"></A>
|
|
<A NAME="sec:oniomeg2"></A>
|
|
<BR>
|
|
23.6.2 Optimization and frequencies
|
|
</H2>
|
|
A two-layer model including modification of theory, basis, ECP and
|
|
total charge and no link atoms.
|
|
|
|
<P>
|
|
This input reproduces the ONIOM optimization and vibrational frequency
|
|
calculation of <IMG
|
|
WIDTH="91" HEIGHT="31" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img182.gif"
|
|
ALT="$Rh(CO)_2Cp$"> of Dapprich et al. The model system is
|
|
<IMG
|
|
WIDTH="74" HEIGHT="35" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img183.gif"
|
|
ALT="$Rh(CO)_2^+$">. The low theory is the Gaussian LANL2MB model (Hay-Wadt
|
|
n+1 ECP with minimal basis on Rh, STO-3G on others) with SCF. The
|
|
high theory is the Gaussian LANL2DZ model (another Hay-Wadt ECP with a
|
|
DZ basis set on Rh, Dunning split valence on the other atoms) with
|
|
DFT/B3LYP. Note that different names should be used for the basis set
|
|
and ECP since the same mechanism is used to store them in the
|
|
database.
|
|
|
|
<P>
|
|
<PRE>
|
|
start
|
|
|
|
ecp LANL2DZ_ECP
|
|
rh library LANL2DZ_ECP
|
|
end
|
|
|
|
basis LANL2DZ spherical
|
|
rh library LANL2DZ_ECP
|
|
o library SV_(Dunning-Hay); c library SV_(Dunning-Hay); h library SV_(Dunning-Hay)
|
|
end
|
|
|
|
ecp Hay-Wadt_MB_(n+1)_ECP
|
|
rh library Hay-Wadt_MB_(n+1)_ECP
|
|
end
|
|
|
|
# This is the minimal basis used by Gaussian. It is not the same
|
|
# as the one in the EMSL basis set library for this ECP.
|
|
basis Hay-Wadt_MB_(n+1) spherical
|
|
Rh s; .264600D+01 -.135541D+01; .175100D+01 .161122D+01; .571300D+00 .589381D+00
|
|
Rh s; .264600D+01 .456934D+00; .175100D+01 -.595199D+00; .571300D+00 -.342127D+00
|
|
.143800D+00 .410138D+00; .428000D-01 .780486D+00
|
|
Rh p; .544000D+01 -.987699D-01; .132900D+01 .743359D+00; .484500D+00 .366846D+00
|
|
Rh p; .659500D+00 -.370046D-01; .869000D-01 .452364D+00; .257000D-01 .653822D+00
|
|
Rh d; .366900D+01 .670480D-01; .142300D+01 .455084D+00; .509100D+00 .479584D+00
|
|
.161000D+00 .233826D+00
|
|
o library sto-3g; c library sto-3g; h library sto-3g
|
|
end
|
|
|
|
charge 0
|
|
geometry autosym
|
|
rh 0.00445705 -0.15119674 0.00000000
|
|
c -0.01380554 -1.45254070 1.35171818
|
|
c -0.01380554 -1.45254070 -1.35171818
|
|
o -0.01805883 -2.26420212 2.20818932
|
|
o -0.01805883 -2.26420212 -2.20818932
|
|
c 1.23209566 1.89314720 0.00000000
|
|
c 0.37739392 1.84262319 -1.15286640
|
|
c -1.01479160 1.93086461 -0.70666350
|
|
c -1.01479160 1.93086461 0.70666350
|
|
c 0.37739392 1.84262319 1.15286640
|
|
h 2.31251453 1.89903673 0.00000000
|
|
h 0.70378132 1.86131979 -2.18414218
|
|
h -1.88154273 1.96919306 -1.35203550
|
|
h -1.88154273 1.96919306 1.35203550
|
|
h 0.70378132 1.86131979 2.18414218
|
|
end
|
|
|
|
dft; grid fine; convergence gradient 1e-6 density 1e-6; xc b3lyp; end
|
|
scf; thresh 1e-6; end
|
|
|
|
oniom
|
|
low scf basis Hay-Wadt_MB_(n+1) ecp Hay-Wadt_MB_(n+1)_ECP
|
|
high dft basis LANL2DZ ecp LANL2DZ_ECP
|
|
model 5 charge 1
|
|
print low
|
|
end
|
|
|
|
task oniom optimize
|
|
task oniom freq
|
|
</PRE>
|
|
|
|
<P>
|
|
|
|
<H2><A NAME="SECTION002563000000000000000"></A>
|
|
<A NAME="sec:oniomeg3"></A>
|
|
<BR>
|
|
23.6.3 A three-layer example
|
|
</H2>
|
|
|
|
<P>
|
|
A three layer example combining CCSD(T), and MP2 with two different
|
|
quality basis sets, and using multiple link atoms.
|
|
|
|
<P>
|
|
The full system is tetra-dimethyl-amino-ethylene (TAME) or
|
|
(N(Me)2)2-C=C-(N(Me)2)2. The intermediate system is (NH2)2-C=C-(NH2)2
|
|
and H2C=CH2 is the model system. CCSD(T)+aug-cc-pvtz is used for the
|
|
model region, MP2+aug-cc-pvtz for the intermediate region, and
|
|
MP2+aug-cc-pvdz for everything.
|
|
|
|
<P>
|
|
In the real geometry the first two atoms (C, C) are the model system
|
|
(link atoms will be added automatically). The first six atoms (C, C,
|
|
N, N, N, N) describe the intermediate system (again with link atoms to
|
|
be added automatically). The atoms have been numbered using comments
|
|
to make the bonding input easier to generate.
|
|
|
|
<P>
|
|
To make the model system, four C-N bonds are broken between the
|
|
ethylene fragment and the dimethyl-amino groups and replaced with C-H
|
|
bonds. To make the intermediate system, eight C-N bonds are broken
|
|
between the nitrogens and the methyl groups and replaced with N-H
|
|
bonds. The scaling factor could be chosen differently for each of the
|
|
bonds.
|
|
|
|
<P>
|
|
<PRE>
|
|
start
|
|
|
|
geometry
|
|
C 0.40337795 -0.17516305 -0.51505208 # 1
|
|
C -0.40328664 0.17555927 0.51466084 # 2
|
|
N 1.87154979 -0.17516305 -0.51505208 # 3
|
|
N -0.18694782 -0.60488524 -1.79258692 # 4
|
|
N 0.18692927 0.60488318 1.79247594 # 5
|
|
N -1.87148219 0.17564718 0.51496494 # 6
|
|
C 2.46636552 1.18039452 -0.51505208 # 7
|
|
C 2.48067731 -1.10425355 0.46161675 # 8
|
|
C -2.46642715 -1.17982091 0.51473105 # 9
|
|
C -2.48054940 1.10495864 -0.46156202 # 10
|
|
C 0.30027136 0.14582197 -2.97072148 # 11
|
|
C -0.14245927 -2.07576980 -1.96730852 # 12
|
|
C -0.29948109 -0.14689874 2.97021079 # 13
|
|
C 0.14140463 2.07558249 1.96815181 # 14
|
|
H 0.78955302 2.52533887 1.19760764
|
|
H -0.86543435 2.50958894 1.88075113
|
|
... and 22 other hydrogen atoms on the methyl groups
|
|
end
|
|
|
|
basis aug-cc-pvtz spherical
|
|
C library aug-cc-pvtz; H library aug-cc-pvtz
|
|
end
|
|
|
|
basis aug-cc-pvdz spherical
|
|
C library aug-cc-pvtz; H library aug-cc-pvtz
|
|
end
|
|
|
|
oniom
|
|
high ccsd(t) basis aug-cc-pvtz
|
|
medium mp2 basis aug-cc-pvtz
|
|
low mp2 basis aug-cc-pvdz
|
|
model 2 1 3 0.87 1 4 0.87 2 5 0.87 2 6 0.87
|
|
|
|
inter 6 3 7 0.69 3 8 0.69 4 11 0.69 4 12 0.69 \
|
|
5 13 0.69 5 14 0.69 6 9 0.69 6 10 0.69
|
|
end
|
|
|
|
task oniom
|
|
</PRE>
|
|
|
|
<P>
|
|
|
|
<H2><A NAME="SECTION002564000000000000000"></A>
|
|
<A NAME="sec:oniomeg4"></A>
|
|
<BR>
|
|
23.6.4 DFT with and without charge fitting
|
|
</H2>
|
|
Demonstrates use of general input strings.
|
|
|
|
<P>
|
|
A two-layer model for anthracene (a linear chain of three fused benzene
|
|
rings) using benzene as the model system. The high-level theory is
|
|
DFT/B3LYP/TZVP with exact Coulomb. The low level is DFT/LDA/DZVP2 with
|
|
charge fitting.
|
|
|
|
<P>
|
|
Note the following.
|
|
|
|
<OL>
|
|
<LI>The semi-colons and quotation marks inside the input string must be
|
|
quoted with backslash.
|
|
</LI>
|
|
<LI>The low level of theory sets the fitting basis set and the high level of
|
|
theory unsets it.
|
|
</LI>
|
|
</OL>
|
|
|
|
<P>
|
|
<PRE>
|
|
start
|
|
geometry
|
|
symmetry d2h
|
|
C 0.71237329 -1.21458940 0.0
|
|
C -0.71237329 -1.21458940 0.0
|
|
C 0.71237329 1.21458940 0.0
|
|
C -0.71237329 1.21458940 0.0
|
|
C -1.39414269 0.00000000 0.0
|
|
C 1.39414269 0.00000000 0.0
|
|
H -2.47680865 0.00000000 0.0
|
|
H 2.47680865 0.00000000 0.0
|
|
C 1.40340535 -2.48997027 0.0
|
|
C -1.40340535 -2.48997027 0.0
|
|
C 1.40340535 2.48997027 0.0
|
|
C -1.40340535 2.48997027 0.0
|
|
C 0.72211503 3.64518615 0.0
|
|
C -0.72211503 3.64518615 0.0
|
|
C 0.72211503 -3.64518615 0.0
|
|
C -0.72211503 -3.64518615 0.0
|
|
H 2.48612947 2.48094825 0.0
|
|
H 1.24157357 4.59507342 0.0
|
|
H -1.24157357 4.59507342 0.0
|
|
H -2.48612947 2.48094825 0.0
|
|
H 2.48612947 -2.48094825 0.0
|
|
H 1.24157357 -4.59507342 0.0
|
|
H -1.24157357 -4.59507342 0.0
|
|
H -2.48612947 -2.48094825 0.0
|
|
end
|
|
|
|
basis small
|
|
h library DZVP_(DFT_Orbital)
|
|
c library DZVP_(DFT_Orbital)
|
|
end
|
|
|
|
basis fitting
|
|
h library DGauss_A1_DFT_Coulomb_Fitting
|
|
c library DGauss_A1_DFT_Coulomb_Fitting
|
|
end
|
|
|
|
basis big
|
|
h library TZVP_(DFT_Orbital)
|
|
c library TZVP_(DFT_Orbital)
|
|
end
|
|
|
|
oniom
|
|
model 8 1 9 0.75 2 10 0.75 3 11 0.75 4 12 0.75
|
|
high dft basis big input "unset \"cd basis\"\; dft\; xc b3lyp\; end"
|
|
low dft basis small input "set \"cd basis\" fitting\; dft\; xc\; end"
|
|
end
|
|
|
|
task oniom
|
|
</PRE>
|
|
|
|
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|
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<ADDRESS>
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Edoardo Apra
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2004-05-25
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