mirror of
https://github.com/nwchemgit/nwchem.git
synced 2026-07-24 03:55:30 -04:00
97f303e6f8
automatically be expanded to include useful information about the checkin (including the file's revision number). With the switch over to SVN this was lost because SVN only does this expansion if you explicitly ask for it (for every single file). I have added a script to the contrib directory that sets the appropriate property to get SVN to do this expansion. This script will make it easy to do this every time new source files are added. It is called svn_expand_Id, the script contains some comments that explain the issue and how it addresses this. This checkin sets this property for a subset of the relevant files (trying to commit all files at once failed with svn crashing). In future the script will only affect those files for which the property was not set before.
240 lines
6 KiB
TeX
240 lines
6 KiB
TeX
%
|
|
% $Id$
|
|
%
|
|
\label{sec:dplot}
|
|
\begin{verbatim}
|
|
DPLOT
|
|
...
|
|
END
|
|
\end{verbatim}
|
|
|
|
This directive is used to obtain the plots of various types of electron
|
|
densities (or orbitals) of the molecule. The electron density is calculated
|
|
on a specified set of grid points using the molecular orbitals
|
|
from SCF or DFT calculation. The output file is either in
|
|
\htmladdnormallink{MSI Insight II}
|
|
{http://www.msi.com/materials/insight/Insight2.html} contour format
|
|
(default)
|
|
or in the
|
|
\htmladdnormallink{Gaussian Cube}{http://www.gaussian.com/g_ur/u_cubegen.htm}
|
|
format. DPLOT is not executed until the ``\verb+task dplot+'' directive is given.
|
|
Different sub-directives are described below.
|
|
|
|
\section{{\tt GAUSSIAN} --- Gaussian Cube format}
|
|
|
|
\begin{verbatim}
|
|
GAUSSIAN
|
|
\end{verbatim}
|
|
|
|
A outputfile is generate in Gaussian Cube format.
|
|
You can visualize this file using \htmladdnormallink{gOpenMol}
|
|
{http://www.csc.fi/gopenmol/tutorials/quick_start.phtml\#view}
|
|
(after converting the Gaussian Cube file with
|
|
\htmladdnormallink{gcube2plt}
|
|
{http://www.csc.fi/lul/chem/scarecrow/gcube2plt.c}),
|
|
\htmladdnormallink{Molden}
|
|
{http://www.cmbi.kun.nl/~schaft/molden/molden.html}
|
|
or
|
|
\htmladdnormallink{Molekel}
|
|
{http://www.cscs.ch/molekel/}.
|
|
|
|
\section{{\tt TITLE} --- Title directive}
|
|
|
|
\begin{verbatim}
|
|
TITLE <string Title default Unknown Title>
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies a title line for the generated
|
|
input to the {\em Insight} program or for the Gaussian cube
|
|
file. Only one line is allowed.
|
|
|
|
\section{{\tt LIMITXYZ} --- Plot limits}
|
|
|
|
\begin{verbatim}
|
|
LIMITXYZ [units <string Units default angstroms>]
|
|
<real X_From> <real X_To> <integer No_Of_Spacings_X>
|
|
<real Y_From> <real Y_To> <integer No_Of_Spacings_Y>
|
|
<real Z_From> <real Z_To> <integer No_Of_Spacings_Z>
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies the limits of the cell to be plotted.
|
|
The grid is generated using \verb+No_Of_Spacings+~+~\verb+1+ points
|
|
along each direction. The known names for \verb+Units+ are
|
|
\verb+angstroms+, \verb+au+ and \verb+bohr+.
|
|
|
|
|
|
|
|
\section{{\tt SPIN} --- Density to be plotted}
|
|
|
|
\begin{verbatim}
|
|
SPIN <string Spin default total>
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies, what kind of density is to be computed. The
|
|
known names for \verb+Spin+ are \verb+total+, \verb+alpha+, \verb+beta+
|
|
and \verb+spindens+, the last being computed as the difference between
|
|
$\alpha$ and $\beta$ electron densities.
|
|
|
|
|
|
|
|
\section{{\tt OUTPUT} --- Filename}
|
|
|
|
\begin{verbatim}
|
|
OUTPUT <string File_Name default dplot>
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies the name of the generated input to the
|
|
{\em Insight} program or the generated Gaussian cube file.
|
|
The name \verb+OUTPUT+ is reserved for the
|
|
standard NWChem output.
|
|
|
|
|
|
|
|
\section{{\tt VECTORS} --- MO vector file name}
|
|
|
|
\begin{verbatim}
|
|
VECTORS <string File_Name default movecs> [<string File_Name2>]
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies the name of the molecular orbital file.
|
|
If the second file is optionally given the density is computed as the
|
|
difference between the corresponding electron densities. The vector
|
|
files have to match.
|
|
|
|
\section{{\tt DENSMAT} --- Density matrix file name}
|
|
|
|
\begin{verbatim}
|
|
DENSMAT <string File_Name> [<string File_Name2>]
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies the name of density matrix file,
|
|
and used for plotting the density generated by correlation methods,
|
|
such as CCSD for ground state and EOM-CCSD for excited states.
|
|
|
|
The second file is optional. When it is given,
|
|
the difference of the densities, specified by the two density matrix files,
|
|
is computed and plotted.
|
|
|
|
\section{{\tt WHERE} --- Density evaluation}
|
|
|
|
\begin{verbatim}
|
|
WHERE <string Where default grid>
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies where the density is to be computed.
|
|
The known names for \verb+Where+ are \verb+grid+ (the calculation of
|
|
the density is performed on the set of a grid points specified by the
|
|
sub-directive \verb+LimitXYZ+ and the file specified by the sub-directive
|
|
\verb+Output+ is generated), \verb+nuclei+ (the density is computed at
|
|
the position of the nuclei and written to the NWChem output) and
|
|
\verb+g++\verb+n+ (both).
|
|
|
|
|
|
\section{{\tt ORBITAL} --- Orbital sub-space}
|
|
|
|
\begin{verbatim}
|
|
ORBITALS [<string Option default density>]
|
|
<integer No_Of_Orbitals>
|
|
<integer Orb_No_1 Orb_No_2 ...>
|
|
\end{verbatim}
|
|
|
|
This sub-directive specifies the subset of the orbital space for the
|
|
calculation of the electron density. The density is computed using the
|
|
occupation numbers from the orbital file modified according to the
|
|
\verb+Spin+ directive. If the contours of the orbitals are to be plotted
|
|
\verb+Option+ should be set to \verb+view+. Note, that in this case
|
|
\verb+No_Of_Orbitals+ should be set to \verb+1+ and sub-directive
|
|
\verb+Where+ is automatically set to \verb+grid+. Also specification
|
|
of two orbital files conflicts with the \verb+view+ option.
|
|
$\alpha$ orbitals are always plotted unless \verb+Spin+ is set to
|
|
\verb+beta+.
|
|
|
|
\section{Examples}
|
|
|
|
\subsection*{Charge Density}
|
|
|
|
Example of charge density plot (with Gaussian Cube output):
|
|
\begin{verbatim}
|
|
start n2
|
|
geometry
|
|
n 0 0 0.53879155
|
|
n 0 0 -0.53879155
|
|
end
|
|
basis; n library cc-pvdz;end
|
|
scf
|
|
vectors output n2.movecs
|
|
end
|
|
dplot
|
|
TITLE HOMO
|
|
vectors n2.movecs
|
|
LimitXYZ
|
|
-3.0 3.0 10
|
|
-3.0 3.0 10
|
|
-3.0 3.0 10
|
|
spin total
|
|
gaussian
|
|
output lumo.cube
|
|
end
|
|
task scf
|
|
task dplot
|
|
\end{verbatim}
|
|
|
|
\begin{verbatim}
|
|
start n2
|
|
geometry
|
|
n 0 0 0.53879155
|
|
n 0 0 -0.53879155
|
|
end
|
|
basis; n library cc-pvdz;end
|
|
scf
|
|
vectors output n2.movecs
|
|
end
|
|
|
|
tce
|
|
ccsd
|
|
densmat n2.densmat
|
|
end
|
|
|
|
task tce energy
|
|
|
|
dplot
|
|
TITLE HOMO
|
|
LimitXYZ
|
|
-3.0 3.0 10
|
|
-3.0 3.0 10
|
|
-3.0 3.0 10
|
|
spin total
|
|
gaussian
|
|
densmat n2.densmat
|
|
output lumo.cube
|
|
end
|
|
task dplot
|
|
\end{verbatim}
|
|
|
|
\subsection*{Molecular Orbital}
|
|
|
|
Example of orbital plot (with Insight II contour output):
|
|
\begin{verbatim}
|
|
start n2
|
|
geometry
|
|
n 0 0 0.53879155
|
|
n 0 0 -0.53879155
|
|
end
|
|
basis; n library cc-pvdz;end
|
|
scf
|
|
vectors output n2.movecs
|
|
end
|
|
dplot
|
|
TITLE HOMO
|
|
vectors n2.movecs
|
|
LimitXYZ
|
|
-3.0 3.0 10
|
|
-3.0 3.0 10
|
|
-3.0 3.0 10
|
|
spin total
|
|
orbitals view; 1; 7
|
|
output homo.grd
|
|
end
|
|
task scf
|
|
task dplot
|
|
\end{verbatim}
|