readme.lyx

已经编译好的levoo程序

#This file was created by <lev> Mon Feb 11 11:06:55 2002
#LyX 1.0 (C) 1995-1999 Matthias Ettrich and the LyX Team
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\layout Title


\family typewriter 
\series bold 
\emph on 
LEV00
\series default 
\emph default 
 & 
\series bold 
\emph on 
TETR
\family default 
\series default 
\emph default 
: User-friendly package for plane-waved DFT codes 
\family typewriter 
\series bold 
CASTEP
\series default 
/
\series bold 
CETEP
\series default 
/
\series bold 
VASP
\family default 
\series default 
 
\layout Author

L.
 N.
 Kantorovich 
\layout 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.
 
\layout Standard


\begin_inset LatexCommand \tableofcontents{}

\end_inset 


\layout Section

Introduction
\layout Standard

The original idea of this package was simply to facilitate the calculation
 of the Density of States (DOS), including local DOS (LDOS), after a 
\series bold 
CASTEP
\series default 
 run.
 As the code developed and new problems arose, many other options have been
 added including 
\series bold 
CETEP
\series default 
 and 
\series bold 
VASP
\series default 
 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 
\family typewriter 
GNUPLOT 
\family default 
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-friendl
y, 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.
 
\layout Standard

The most sophisticated support is provided for the 
\series bold 
CASTEP
\series default 
 code.
 Some minor changes should be made, however, in the 
\series bold 
CASTEP
\series default 
 to make it compatible.
 The same is true for the 
\series bold 
CETEP
\series default 
.
 However, no changes to 
\series bold 
VASP
\series default 
 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 on 
 
\noun default 
the latest version before using this package.
 For brevity, all these codes will be called PW (plane-wave) codes.
\layout Standard

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

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

Menus
\layout Standard

The main codes 
\series bold 
tetr
\series default 
 and 
\series bold 
lev00
\series default 
, as well as some others (
\series bold 
do_param
\series default 
, 
\series bold 
lev1
\series default 
, 
\series bold 
lev2
\series default 
) 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!
\layout Section

Brief description of utilities which make up the package
\layout Standard

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.
\layout Subsection

General utilities
\layout Itemize


\series bold 
tetr
\series default 
 
\begin_inset Formula \( \rightarrow  \)
\end_inset 

 an interactive menu-driven program which enables you: 
\begin_deeper 
\layout Itemize

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;
\layout Itemize

to check the point group of the system
\layout Itemize

to create a 
\begin_inset Formula \( \mathbf{k} \)
\end_inset 

-point file for DOS (with complete account of the point symmetry of the
 cell), ground state or band-structure calculations;
\layout Itemize

Coulomb potential at an arbitrary point in the cell in the point-ion approximati
on,
\layout Itemize

some additional useful options designed to analyze the system geometry e.g.
 after the relaxation (distances, breeding atoms, etc.)
\layout Itemize

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.
\layout Itemize

PES: move atoms in the cell keeping the symmetry: this is useful for calculating
 the potential energy surfaces (PES) for the given symmetry.
\layout Itemize

full support of 
\series bold 
VASP
\series default 
,
\series bold 
 
\series default 
for academia 
\series bold 
CASTEP
\series default 
, 
\series bold 
CETEP
\end_deeper 
\layout Itemize


\series bold 
lev00
\series default 
 
\begin_inset Formula \( \rightarrow  \)
\end_inset 

 an interactive menu-driven (and quite intelligent!) program with quite
 a few applications.
 Amongst those: 
\begin_deeper 
\layout Itemize

Charge/spin/partial densities:
\begin_deeper 
\layout Itemize

plot of charge/spin densities or partial charge densities along a line (1-dimens
ional) or in a plane (2-dimensional) in the cell;
\layout Itemize

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;
\layout Itemize

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!
\layout Itemize

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.)
\layout Itemize

dipole, quadrupole moment of the cell
\layout Itemize

plot of 
\begin_inset Formula \( z \)
\end_inset 

-dependent partial charge densities for each state against the 
\begin_inset Formula \( z \)
\end_inset 

-side of the slab to see immediately which states are localised near its
 edges (
\shape italic 
surface
\shape default 
 states) and which of them are mostly localised inside the slab (
\shape italic 
bulk
\shape default 
 states);
\layout Itemize

construction of a general linear combination of two charge densities; for
 example, one can subtract one density from another;
\layout Itemize

recalculation of the charge density with respect to a new position of the
 coordinate system (
\shape italic 
shift
\shape default 
); 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 
\begin_inset Formula \( \mathbf{k} \)
\end_inset 

-points.
 Therefore, one has to shift the system and recalculate the density 
\shape italic 
prior
\shape default 
 to the band-structure run of the PW code.
 
\end_deeper 
\layout Itemize

DOS/LDOS applications:
\begin_deeper 
\layout Itemize

plot of the total and projected DOS (calculated either in 
\emph on 
DOS 
\emph default 
or 
\emph on 
DOp
\emph default 
 regimes of 
\series bold 
lev1
\series default 
 or 
\series bold 
CETEP
\series default 
) 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 
\series bold 
VASP
\series default 
.
\layout Itemize

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_deeper 
\layout Itemize

plotting of the total Coulomb potential (including the electronic part)
 across the cell.
\layout Itemize

full support for old 
\series bold 
CASTEP 
\series default 
and 
\series bold 
CETEP
\series default 
 (some additional modification of those are needed though); all major options
 for
\series bold 
 VASP
\series default 
 are also fully supported, no modifications are required.
\layout Itemize

in all cases the information obtained can be previewed using 
\family typewriter 
GNUPLOT
\family default 
 directly from 
\series bold 
lev00
\series default 
 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_deeper 
\layout Subsection

Utilities used only by CASTEP
\layout Itemize


\series bold 
lev1 
\series default 

\begin_inset Formula \( \rightarrow  \)
\end_inset 

 an interactive menu-driven utility; it needs files with wavefunctions at
 all 
\begin_inset Formula \( \mathbf{k} \)
\end_inset 

-points generated by 
\series bold 
CASTEP
\series default 
 and then calculates an intermediate file 
\family typewriter 
psi2.[option]
\family default 
 for one of the options 
\emph on 
DOS
\emph default 
, 
\emph on 
DOp
\emph default 
, 
\emph on 
SRF
\emph default 
 or 
\emph on 
MAP
\emph default 
:
\begin_deeper 
\layout Itemize

calculate the total DOS, LDOS projected onto spheres as well as LDOS projected
 on a 
\begin_inset Formula \( s \)
\end_inset 

, 
\begin_inset Formula \( p \)
\end_inset 

, 
\begin_inset Formula \( d \)
\end_inset 

-like AO (the 
\emph on 
DOS
\emph default 
 option);
\layout Itemize

calculate LDOS projected to thin layers (the option 
\emph on 
DOp
\emph default 
); this is useful for analysing structure of surface states in the case
 of slab calculations;
\layout Itemize

calculate and store partial charge densities in the real space for the specific
 range of states (the 
\emph on 
MAP
\emph default 
 option);
\layout Itemize

for the slab calculations, calculate and store 
\begin_inset Formula \( z \)
\end_inset 

-dependent partial charge densities which are partial charge densities integrate
d in the 
\begin_inset Formula \( xy \)
\end_inset 

-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 on 
SRF
\emph default 
 option).
\layout Standard

Eigenvalues calculated on the last iteration of the band-structure run of
 the 
\series bold 
CASTEP
\series default 
 are to be printed out into a special file called 
\family typewriter 
band.out
\family default 
.
 On the last stage, files 
\family typewriter 
band.out
\family default 
 and 
\family typewriter 
psi2.[option]
\family default 
 are used to calculate and plot DOS, LDOS, wavefunctions or partial charge
 densities by running a special utility 
\series bold 
lev00
\series default 
.
 
\end_deeper 
\layout Itemize


\series bold 
check
\series default 
 
\begin_inset Formula \( \rightarrow  \)
\end_inset 

 (is probably redundant by now) reads 
\shape italic 
all
\shape default 
 files needed to run the 
\series bold 
CASTEP
\series default 
 and tells the user: 
\begin_deeper 
\layout Itemize

whether all the parameters in the 
\family typewriter 
param.inc
\family default