readme.tex

已经编译好的levoo程序

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\title{\texttt{\textbf{\emph{LEV00}}} \texttt{\&} \texttt{\textbf{\emph{TETR}}}: User-friendly
package for plane-waved DFT codes \texttt{\textbf{CASTEP}}\texttt{/}\texttt{\textbf{CETEP}}\texttt{/}\texttt{\textbf{VASP}} }


\author{L. N. Kantorovich }

\maketitle
\begin{abstract}
This is a part of the documentation for a package of utilities which have been
written at Keele (and then continued in London at UCL) to help to prepare the
input to and then to work out the output of the plane wave DFT code CASTEP and
CETEP. At the later stage almost complete support for the VASP code has been
also added and then the whole structure has been reshuffled in order to allow
for a more flexible support for other codes and formats. The applications (i.e.
offered functionality) include calculations of the Density of States (DOS),
a powerful engine for generation of supercells, plotting of charge densities
and wavefunctions, calculation of charges on atoms from the electronic density,
an intelligent search for surface states, exploration of the (partial) electronic
(spin) density, etc. 
\end{abstract}
\tableofcontents{}


\section{Introduction}

The original idea of this package was simply to facilitate the calculation of
the Density of States (DOS), including local DOS (LDOS), after a \textbf{CASTEP}
run. As the code developed and new problems arose, many other options have been
added including \textbf{CETEP} and \textbf{VASP} support. Now the real purpose
of the package is really to accompany any grid based plane wave DFT code (like
those mentioned above) in various aspects. At the moment the package can be
used on many computers where graphical package \texttt{GNUPLOT} is available.
Some tricks developed in the code (like the internal write/read statements,
for example, or reading from the command line) which make the code user-friendly,
may be platform-dependent, but it runs at least on PCs with Linux and on DEC.
Make-files are available for these platforms so that some changes might be necessary
if other platforms are to be used. 

The most sophisticated support is provided for the \textbf{CASTEP} code. Some
minor changes should be made, however, in the \textbf{CASTEP} to make it compatible.
The same is true for the \textbf{CETEP}. However, no changes to \textbf{VASP}
are necessary at present at the expense that LDOS can be calculated only on
atoms. Please, contact the distributors of these codes for getting \noun{}the
latest version before using this package. For brevity, all these codes will
be called PW (plane-wave) codes.

I recommend to put all the source in the directory \texttt{\~{/}TOOLS} in your
home directory and all necessary scripts (provided) - in your \texttt{\~{/}bin}
directory. If you have done this, the scripts should work straight away. 

The package consists of several codes which are described in some detail in
this document in a proper section. A fairly \textit{short} description of each
utility is also given in the next section for the reader's convenience.


\subsection{Menus}

The main codes \textbf{tetr} and \textbf{lev00}, as well as some others (\textbf{do\_param},
\textbf{lev1}, \textbf{lev2}) are menu driven. All menus work in a very simple
and straightforward fashion: every menu item has either a number or a symbol.
You see on the screen the whole menu. To execute a particular option you press
the number (symbol). Normally this would cause some kind of calculation and
the original menu would reappear (it may be different now!), so that something
else can be done. In some other cases choosing an option invokes a different
menu (sub-menu) or may change some settings - you should notice it when the
original menu reappears!


\section{Brief description of utilities which make up the package}

In this section we provide a brief description of every utility which the package
consists from. This will allow you to understand a general strategy and get
most of the package. We also introduce some special terminology which is used
throughout the document. Then you can turn to a proper section of the document
where each utility is considered in some detail.


\subsection{General utilities}

\begin{itemize}
\item \textbf{tetr} \( \rightarrow  \) an interactive menu-driven program which enables
you: 

\begin{itemize}
\item Create the geometry file by e.g. extending the primitive cell, taking out atoms,
checking for equivalent ones (is useful in complicated cases of e.g. steps,
kinks, corners, etc.); rotating and/or shift the system; adding/removing atoms
from the existing cell; it has also a powerful engine for building surfaces
from the bulk cells;
\item to check the point group of the system
\item to create a \( \mathbf{k} \)-point file for DOS (with complete account of the
point symmetry of the cell), ground state or band-structure calculations;
\item Coulomb potential at an arbitrary point in the cell in the point-ion approximation,
\item some additional useful options designed to analyze the system geometry e.g.
after the relaxation (distances, breeding atoms, etc.)
\item make distorted geometries for studying vibrations of molecules for particular
vibrational modes; fully symmetry adapted; this is done using the group theory;
rotations and translations of molecules are automatically eliminated.
\item PES: move atoms in the cell keeping the symmetry: this is useful for calculating
the potential energy surfaces (PES) for the given symmetry.
\item full support of \textbf{VASP}, \textbf{}for academia \textbf{CASTEP}, \textbf{CETEP}
\end{itemize}
\item \textbf{lev00} \( \rightarrow  \) an interactive menu-driven (and quite intelligent!)
program with quite a few applications. Amongst those: 

\begin{itemize}
\item Charge/spin/partial densities:

\begin{itemize}
\item plot of charge/spin densities or partial charge densities along a line (1-dimensional)
or in a plane (2-dimensional) in the cell;
\item exploration of the charge densities: it seeks peaks and gives their positions
in the space of the cell, heights, amount of charge involved, etc.; this has
been proved to be especially useful for studying partial charge densities or
wave functions for particular states in the direct space which were thought
to be responsible for particular interesting features in the LDOS;
\item integration of the (partial) charge densities over a set of spheres of given
radii; this allows you to gain an idea about the chemical nature of bonding
in the system, charges on atoms, etc.; note that spheres may overlap so that
you can construct a quite sophisticated region in space to study the density!
\item one can cut parts of the density out, simulate it by point charges; this is
useful if a complimentary simulation is to be done (e.g. dipole correction,
polarisation calculation for a defect outside the cell, etc.)
\item dipole, quadrupole moment of the cell
\item plot of \( z \)-dependent partial charge densities for each state against the
\( z \)-side of the slab to see immediately which states are localised near
its edges (\textit{surface} states) and which of them are mostly localised inside
the slab (\textit{bulk} states);
\item construction of a general linear combination of two charge densities; for example,
one can subtract one density from another;
\item recalculation of the charge density with respect to a new position of the coordinate
system (\textit{shift}); this is necessary if the ground state calculation charge
density has been obtained for a lower symmetry position and the band-structure
calculation is necessary (for the DOS, for instance) when the symmetry is crucial
to reduce the number of \( \mathbf{k} \)-points. Therefore, one has to shift
the system and recalculate the density \textit{prior} to the band-structure
run of the PW code. 
\end{itemize}
\item DOS/LDOS applications:

\begin{itemize}
\item plot of the total and projected DOS (calculated either in \emph{DOS} or \emph{DOp}
regimes of \textbf{lev1} or \textbf{CETEP}) for various choices of groups of
states (or for the whole set of those) using the method of tetrahedra; one can
preview several curves at the time for different choices of groups of states;
this last option is especially useful for identification of peaks in the LDOS;
only DOS and LDOS on atoms is presently supported for \textbf{VASP}.
\item the DOS/LDOS can be smeared (convoluted) by integrating it (numerically or analytically)
with a Gaussian function of a specific dispersion; there is also a possibility
to play around with various dispersions for the Gaussian smearing and compare
them by previewing the DOS. 
\end{itemize}
\item plotting of the total Coulomb potential (including the electronic part) across
the cell.
\item full support for old \textbf{CASTEP} and \textbf{CETEP} (some additional modification
of those are needed though); all major options for \textbf{VASP} are also fully
supported, no modifications are required.
\item in all cases the information obtained can be previewed using \texttt{GNUPLOT}
directly from \textbf{lev00} in a form of 1- or 2-dimensional plots. It can
be checked, corrected (e.g., the position of the plane for a 2-dimensional plot)
previewed again and then finally printed out to data and/or Postscript files.
\end{itemize}
\end{itemize}

\subsection{Utilities used only by CASTEP}

\begin{itemize}
\item \textbf{lev1} \( \rightarrow  \) an interactive menu-driven utility; it needs
files with wavefunctions at all \( \mathbf{k} \)-points generated by \textbf{CASTEP}
and then calculates an intermediate file \texttt{psi2.{[}option{]}} for one
of the options \emph{DOS}, \emph{DOp}, \emph{SRF} or \emph{MAP}:

\begin{itemize}
\item calculate the total DOS, LDOS projected onto spheres as well as LDOS projected
on a \( s \), \( p \), \( d \)-like AO (the \emph{DOS} option);
\item calculate LDOS projected to thin layers (the option \emph{DOp}); this is useful
for analysing structure of surface states in the case of slab calculations;
\item calculate and store partial charge densities in the real space for the specific
range of states (the \emph{MAP} option);
\item for the slab calculations, calculate and store \( z \)-dependent partial charge
densities which are partial charge densities integrated in the \( xy \)-plane
parallel to the surface of the slab; this is the simplest way to distinguish
surface and bulk states in your slab system (the \emph{SRF} option).
\end{itemize}
Eigenvalues calculated on the last iteration of the band-structure run of the
\textbf{CASTEP} are to be printed out into a special file called \texttt{band.out}.
On the last stage, files \texttt{band.out} and \texttt{psi2.{[}option{]}} are
used to calculate and plot DOS, LDOS, wavefunctions or partial charge densities
by running a special utility \textbf{lev00}. 

\item \textbf{check} \( \rightarrow  \) (is probably redundant by now) reads \textit{all}
files needed to run the \textbf{CASTEP} and tells the user: 

\begin{itemize}
\item whether all the parameters in the \texttt{param.inc} file are sufficient for
the present job, e.g. number of plane waves, etc.;
\item whether all input files are okay and consistent with each other and with the
parameters in the \texttt{param.inc} file.
\item allows you to choose the least necessary parameters to suppress as much as possible
the size of the \textbf{CASTEP}
\end{itemize}
\item \textbf{take} \( \rightarrow  \) checks the convergence of eigenvalues calculated
by the \textbf{CASTEP} during the band-structure run as well as their correct
order; also, it allows one to choose eigenvalues from any desired iteration;
\item \textbf{sum} \( \rightarrow  \) an utility which allows you to split one big
\textbf{CASTEP} job as a sequence of smaller jobs which less \( \mathbf{k} \)-points.
; if files, produced at each run, are properly named, then the utility \textbf{sum}
will ``gather'' the files and will produce the resulting file(s) \texttt{psi2.{[}option{]}}
and \texttt{band.out} corresponding to just one (big) run of \textbf{CASTEP}.