manual_3.93a.lyx

已经编译好的levoo程序

builds a cluster from the bulk cell atomic positions; can terminate some
 or all of the cluster boundary atoms with H atoms;
\layout Itemize

controls calculation of molecular or lattice vibrations taking into account
 irreducible representations of the system (either the point group or the
 group of internal translations within the supercell); in the case of a
 molecule, translations and rotations of the molecule as a whole are automatical
ly eliminated; can do phonon DOS, animations of normal modes, recalculate
 the phonons for different isotops (keeping the same force constant matrix);
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creates 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-points for the ground state (Manchorst-Pack), DOS (the tetrahedral method
 with complete account of the point symmetry of the cell) or band-structure
 calculations (along a chosen line in the Brillouin zone);
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calculates the Coulomb (Ewald) potential at an arbitrary point in the cell
 in the point-ion approximation,
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some additional useful options designed to analyze the system geometry:
 compare with other geometry files, e.g.
 before and after relaxation; a calculator of interatomic distances; check
 a point in the cell for equivalence with existing atoms; save atomic positions
 within a box across adjacent unit cells 
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PES: move atoms in the cell keeping the point symmetry: this is useful for
 calculating the potential energy surfaces (PES) for the ground state symmetry.
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Installation and general information
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The code 
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tetr
\series default 
\emph default 
 must be compiled only once by performing the command 
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make
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in your
\noun on 
 
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\noun default 
~/TOOLS/TETR
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 directory
\noun on 
.

\noun default 
 
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An environmental variable 
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$HOME_TETR
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 must be set to the correct location of the 
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\emph on 
tetr
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\emph default 
 directory, e.g.
 
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setenv HOME_TETR ~/TOOLS/TETR
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for the csh or tcsh shells, or 
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export HOME_TETR=~/TOOLS/TETR
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\align left 
in the case of the bash shell.
 To solve this problem once and forever, put the right statement in the
 
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.cshrc
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 or 
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.bashrc
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 files, respectively.
 The statement will be executed automatically (and the variable set) every
 time an 
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xterm
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 is started or at the login.
 To force the setting from an existing terminal window, run the 
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source
\family default 
 command (e.g.
 
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source ~/.cshrc
\family default 
).
 
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Menus in 
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tetr
\begin_inset LatexCommand \label{sec:Menus-in-tetr}

\end_inset 


\layout Standard

Most of the menus have common options:
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Co
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 - (info) show a table with Cartesian and fractional coordinates of all
 atoms in the unit cell
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S
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 - save the current geometry into an input file (the code format to be chosen
 next)
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Sy
\series default 
 - (info) show (usually, the point) symmetry of the current geometry; in
 most cases the lattice translations are also included, i.e.
 two points are thought to be equivalent if they are separated by a lattice
 translation
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U
\series default 
 - undo the last step
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\series bold 
An
\series default 
 - (setting) choose the format in which coordinates are to be specified
 for input in the menus: Angstrom, fractional or atom number (in order of
 atoms in the system)
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A number of options of the main menu allows a user to change the current
 geometry in various ways.
 The code allows the user then to dump the geometry manually or automatically
 when a change is made.
 When this happens, a file 
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geom.xyz
\family default 
 is written in the 
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xyz
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 format.
 If you run any 
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xyz
\family default 
-file previewer (like e.g.
 
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\emph on 
Xmol
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\emph default 
), then you can preview the system during the modification process that
 is extremely useful.
 A number of options (mainly settings) control this:
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XY
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 - (setting) the format of the 
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geom.xyz
\family default 
 file (either for 
\series bold 
\emph on 
Xmol
\series default 
\emph default 
,
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\emph on 
Ymol
\series default 
\emph default 
 or disable); in the latter case the file will not be written after each
 change of the geometry 
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Hs
\series default 
 - (setting) either add or not H atoms to the 
\family typewriter 
geom.xyz
\family default 
 file to preview x,y,z axes (necessary for 
\series bold 
\emph on 
Xmol
\series default 
\emph default 
 as it does not have the axes facility)
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Bb
\series default 
 - (setting) breeding box is specified: this option allows you to preview
 not just the cell, but 
\begin_inset Formula $N_{1}\times N_{2}\times N_{3}$
\end_inset 

 extention of it; note, that the actual cell is not changed, this option
 only affects the atoms written to the 
\family typewriter 
geom.xyz
\family default 
 file 
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W
\series default 
 - force writing 
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geom.xyz
\family default 
 file for the current geometry
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Normally, when choosing a set of atoms, two integers are specified, so that
 all atoms with numbers between (and including) them are in the list.
 For instance, choosing 5 and 10 would include atoms 5,6,7,8,9 and 10 into
 the list.
 In some cases a non-contagious list is required, e.g.
 5, 7-10, 15 and 22.
 In this case you can 
\begin_inset Quotes eld
\end_inset 

tag
\begin_inset Quotes erd
\end_inset 

 atoms (option 
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T
\series default 
) by naming all of them and using a dash if all numbers in between are to
 be included, e.g.
 5 7-10 15 22 for the example above.
 Note that once atoms are tagged, pressing 
\series bold 
T
\series default 
 again untages them.
 
\layout Section

Getting started
\begin_inset LatexCommand \label{sec:Getting-started-tetr}

\end_inset 


\layout Standard

When starting the code (e.g.
 type 
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./tetr
\family default 
), it first checks if the variable $HOME_TETR is set correctly:
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......................................................
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......
 TETR is an interface to VASP/SIESTA/etc .......
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......................................................
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>>>>>>>> 1st release: 25.07.1994
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>>>>>>>> Version : 3.92h 
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>>>>>>>> Build : Tue Jun 21 19:39:20 BST 2005 
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>>>>>>>> today : Wed Jul 13 00:52:31 BST 2005 
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......................................................
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......
 inquiries to L.
 Kantorovich .........
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......................................................
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OK! File /home/lev/TOOLS/TETR/tetr exists!
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....
 TETR home directory: /home/lev/TOOLS/TETR
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OK! File /home/lev/TOOLS/TETR/symgrp.rep exists!
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OK! File /home/lev/TOOLS/TETR/collect_forces exists!
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OK! File /home/lev/TOOLS/TETR/get_forces exists!
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..................................................
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It must find the executables 
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\emph on 
tetr
\series default 
\emph default 
 and 
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\emph on 
get_forces
\series default 
\emph default 
, a script 
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collect_forces
\family default 
 and the file 
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symgrp.rep
\family default 
.
 At the same time, the current date and version are shown.
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Next, the following first menu is displayed that prompts a user to choose
 the input format for the geometry, the so-called 
\emph on 
Input-menu
\emph default 
:
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Choose the input format:
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1.
 open input as CASTEP [ *.geom]
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2.
 open input as CETEP / old CASTEP
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3.
 open input as VASP
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4.
 open input as SIESTA [ *.fdf ]
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5.
 open output as SIESTA [ *.XV ]
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6.
 open as XYZ-type file [ *.xyz ]
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7.
 NEW or go directly to the main menu
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8.
 QUIT
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------------>
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Options 
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1
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-
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6
\series default 
 imply existing files of the specified formats; you will then be prompted
 to choose the file name, and the input file will be read in.
 If successful, you will be prompted to the main menu, described in Section
 
\begin_inset LatexCommand \ref{sec:Main-menu-tetr}

\end_inset 

.
 If not (e.g.
 due to an error in the input file or becuase the latter does not exist),
 you will be prompted again to the menu above.
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The option 
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7
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 corresponds to starting from scratch rather then reading an existing input
 file of one of the DFT codes.
 In this case a new input file is to be constructed and then saved in one
 of known formats.
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Symmetry
\begin_inset LatexCommand \label{sec:Symmetry-tetr}

\end_inset 


\layout Standard

The point group symmetry of the system is determined automatically and can
 be checked (option 
\series bold 
Sy
\series default 
 in various menus).
 Normally, translations are also taken into account when checking equivalence
 of atoms, i.e.
 two point in space are thought to be equivalent if they are separated by
 a lattice translation 
\begin_inset Formula $\mathbf{L=}n_{1}\mathbf{a}_{1}+n_{2}\mathbf{a}_{2}+n_{3}\mathbf{a}_{3}$
\end_inset 

 with 
\begin_inset Formula $n_{i}$
\end_inset 

 being integers.
 There are some exceptions though corresponding to 
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molecular
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 properties, specifically options 
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Cl
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 (Section 
\begin_inset LatexCommand \ref{sub:Cl-option-tetr}

\end_inset 

) and 
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Vm
\series default 
 (Section 
\begin_inset LatexCommand \ref{sub:Vm-tetr}

\end_inset 

) of the main menu, when translations are ignored.
 The symmetry is used in many parts of the code.
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At the moment, all symmetry operations are fixed to the axes of the Cartesian
 coordinate system.
 The complete list of the symmetry operations is shown in Figs.
 
\begin_inset LatexCommand \ref{cap:Symmetry-operations-of-Oh}

\end_inset 

 and 
\begin_inset LatexCommand \ref{cap:Symmetry-operations-of-D6h}

\end_inset 

.
\layout Standard


\begin_inset Float figure
wide false
collapsed true

\layout Standard
\align center 

\begin_inset Graphics
	filename Oh.xfig.ps
	display monochrome
	width 15cm

\end_inset 


\layout Caption

Symmetry operations of the 
\begin_inset Formula $O_{h}$
\end_inset 

 group.
\begin_inset LatexCommand \label{cap:Symmetry-operations-of-Oh}

\end_inset 


\end_inset 


\layout Standard


\begin_inset Float figure
wide false
collapsed true

\layout Standard
\align center 

\begin_inset Graphics
	filename D6h.xfig.ps
	display monochrome
	width 15cm

\end_inset 


\layout Caption

Additional symmetry operations due to the D
\begin_inset Formula $_{6h}$
\end_inset 

 group.
\begin_inset LatexCommand \label{cap:Symmetry-operations-of-D6h}

\end_inset 


\end_inset 


\layout Subsection

A note about symmetry
\begin_inset LatexCommand \label{sub:A-note-about-symmetry}

\end_inset 


\layout Standard

The fact that the point group operations are rigidly related to the Cartesian
 axes, the symmetry determined by 
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tetr
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\emph default 
 may not be as rich as it should be.
 On the other hand, in many cases it is useful to have the maximum symmetry
 possible (e.g.
 when generating 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-points for the electronic DOS calculation).
 Therefore, it is advised to maximise the system symmetry by shifting and/or
 rotating the whole cell.
 This can be done in the M-menu, Section 
\begin_inset LatexCommand \ref{sub:M-option-tetr}

\end_inset