manual_3.93a.lyx

已经编译好的levoo程序

 Cluster atoms around particular point
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6.
 Choose unit cell with respect to Miller indices:
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1st 2 lattice vectors will be in the (hkl) plane
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Ex.
 Diagonal "breeding": construct a supercell
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Su.
 General "breeding": construct a supercell
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8.
 Create/modify SLAB: change the 3rd(z) lattice vector
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9.
 Arbitrarily change lattice vectors (e.g.
 for molecules)
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10.
 Manually add an atom to the cell
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Ad.
 Add atoms from another file
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/11.
 Remove a range of atoms from the cell
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12.
 Keep a range of atoms in the cell: remove the rest
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13.
 Rename a range of atoms: change species
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Mv.
 Move a range of atoms to another general position
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Rt.
 Rotate a range of atoms about the X,Y,Z axes
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--------- operations with multiple lists of atoms ------------
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T.
 Tag atoms (specify multiple lists): currently OFF
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-------------- g e n e r a l s e t t i n g s ----------------
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UU.
 ****** RESTORE the original serting ******
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U.
 ********** UNDO the last step *************
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XY.
 Produce <geom.xyz> file after every change for Xmol
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Hs.
 H atoms to be added to <geom.xyz> file: NO
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An.
 [For input] Coordinates are specified in: <AtomNumber>
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Co.
 Show current atomic positions in fractional/Cartesian
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Sy.
 Show the point symmetry
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Bb.
 Set the size of the breeding box for visualisation
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>>>>> Current setting for the breeding box: <<<<<
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[ 0...
 0] x [ 0...
 0] x [ 0...
 0]
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>>>>> extension = 1, # of atoms= 65
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W.
 Write <geom.xyz> file to preview using current breeding
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S.
 Save.
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Q.
 Proceed/Quit
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----------> Choose an appropriate option:
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At the top, the current lattice vectors and species are shown.
 What you can do is explained below: 
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1 
\series default 
- all atoms in the cell will be displaced to a new position, the displacement
 vector will be asked in units corresponding to the setting 
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An
\series default 
 
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2
\series default 
 - similar, but the displacement vector will be calculated from the atomic
 masses
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3
\series default 
 - a rotation of the coordinate system is specified by giving new directions
 for a pair of two existing primitive lattice vectors using the 
\emph on 
existing coordinate system
\emph default 
; of course, the angle between them should be preserved! This may be an
 inconvenience, but in some cases the choice is obvious
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4
\series default 
 - move an atom to an equivalent position by adding lattice vectors to its
 current coordinate; this may be e.g.
 useful when building up a slab
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Rf
\series default 
 - some codes such as 
\series bold 
\emph on 
VASP
\series default 
\emph default 
 change atomic positions in the cell in such a way that their fractional
 coordinates become between 0 and 1; this may be not really wanted since
 after the relaxation (with 
\series bold 
\emph on 
VASP
\series default 
\emph default 
) it may be very difficult to recognise the cell; a cure is here: in this
 option upi will be prompted again to the Input-menu (Section 
\begin_inset LatexCommand \ref{sec:Getting-started-tetr}

\end_inset 

) to read in another input file (e.g.
 before the relaxation) the atomic coordinates in the two geometries will
 be compared and proper lattice vectors applied to the relaxed atoms to
 
\begin_inset Quotes eld
\end_inset 

return
\begin_inset Quotes erd
\end_inset 

 them to the original unit cell
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44
\series default 
 - atoms in the system around a given point (atom) are shown that cluster
 around it; more specifically, the displayed atoms have fractional coordinates
 between -0.5 and 0.5 if the centre of the coordinate system is positioned
 at the chosen atom
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6
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 - after specifying three Miller indices, a new equivalent set of primitive
 translations for the cell is given in which the first two vectors 
\begin_inset Formula $\mathbf{A}_{1}$
\end_inset 

and 
\begin_inset Formula $\mathbf{A}_{2}$
\end_inset 

 lie within the plane characterised by the Miller indices; use the option
 
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3
\series default 
 above to rotate the whole cell so that your plane becomes perpendicular
 to the 
\begin_inset Formula $z$
\end_inset 

 axes (if desired)
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Ex
\series default 
 - extend you cell by elongating the three current primitive translations,
 i.e.
 the transformation matrix of Eq.
 (
\begin_inset LatexCommand \ref{sub:Cl-option-tetr}

\end_inset 

) is diagonal: 
\begin_inset Formula $T_{ij}=\delta_{ij}n_{i}$
\end_inset 

; the three integers 
\begin_inset Formula $n_{i}$
\end_inset 

are to be specified 
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Su
\series default 
 - the current cell is extended using a general transformation matrix 
\begin_inset Formula $\mathbf{T}$
\end_inset 

 
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8
\series default 
 - the third lattice vector can be arbitrarily changed here; this is necessary
 in creating a slab out of a bulk cell assuming that the vacuum gap is opened
 via the third lattice vector; note that atomic positions in the cell will
 not change
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9
\series default 
 - all three lattice vectors can be changed; this may be useful in calculating
 a molecule or a cluster, if the distance between images must be changed;
 of course, atomic positions inside the cell do not change
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10
\series default 
 - an additional atom is added to the cell; its position must be unique,
 otherwise, the atom is not added
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\series bold 
Ad
\series default 
 - similar, but in this case all atoms from another file (that may be written
 even in a different format) can be added to the current system; the Input-menu
 (Section 
\begin_inset LatexCommand \ref{sec:Getting-started-tetr}

\end_inset 

) is called here
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11
\series default 
, 
\series bold 
12
\series default 
 - these two options remove a set of atoms from the cell 
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13
\series default 
 - this renames a set of atoms, i.e.
 it changes their species into another species; this may be useful, e.g.
 in changing the lowermost atoms of the slab into hydrogens to terminate
 properly the slab and thus simulate the bulk at the lower surface
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Mv
\series default 
 - move a set of atoms to another position (Section 
\begin_inset LatexCommand \ref{sub:Mv--Move-atoms}

\end_inset 

)
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Rt
\series default 
 - rotate a set of atoms (Section 
\begin_inset LatexCommand \ref{sub:Rt-Rotate-atoms}

\end_inset 

)
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Normally, a set of atoms is chosen by two atomic numbers, in which case
 all atoms with the numbers
\emph on 
 
\emph default 
in between are also chosen.
 If it is required to have a more complex non-contagious set of atoms in
 the list, use the option 
\series bold 
T
\series default 
, that allows you to do this (see Section 
\begin_inset LatexCommand \ref{sec:Menus}

\end_inset 

).
 Note that all atoms added to the system from another file (option 
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Ad
\series default 
) are tagged automatically, so that you can move and/or rotate them.
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Other useful options (in seetings) include:
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U 
\series default 
- undo the last transformation
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UU
\series default 
 - restore the original geometry (the one with which you entered the M-menu
 initially)
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Once the necessary geometry is created (the lattice vectors, number of atoms
 in species and their positions in space), it can be saved using option
 
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S 
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(Section 
\begin_inset LatexCommand \ref{sub:Save-Read-tetr}

\end_inset 

).
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KP - k-points generation 
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KP-menu
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The corresponding menu for the 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-points (KP-menu) looks like this:
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/-------------------------------------------------
\backslash 

\backslash 

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|.................
 K-point menu ..................|
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\backslash 

\backslash 
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0.
 BULK calculation
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NEW reciprocal lattice vectors (up to 2*PI):
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BJ0(1): 0.09190 0.00000 0.00000
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BJ0(2): 0.00000 0.09190 0.00000
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BJ0(3): 0.00000 0.00000 0.09190
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1.
 DOS 
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2.
 BAND: eigenvalues along a k-direction
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3.
 Self-consistent (ordinary) calculation
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Q.
 Return to the main menu
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Specify the character and press ENTER ------->
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The option 
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0
\series default 
 allows one to choose between bulk and slab calculation.
 It is assumed here that the vacuum gap between slabs runs along the third
 lattice vector 
\begin_inset Formula $\mathbf{a}_{3}$
\end_inset 

.
 Although this vector may not be very large in actual calculation, in most
 cases related to the reciprocal space, it is convenient to assume that
 it is of an infinite length.
 This in turn implies that the Brillouin zone (BZ) in the case of a slab
 calculations is effectively 2D (planar, compressed in the third dimension).
 Thus, any 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-point to be constructed in this menu will have its component along the
 third reciprocal vector 
\begin_inset Formula $\mathbf{b}_{3}$
\end_inset 

 (the reciprocal and direct primitive translation vectors are related via
 
\begin_inset Formula $\mathbf{a}_{i}\mathbf{b}_{j}=2\pi\delta_{i,j}$
\end_inset 

) removed, i.e.
 only 
\begin_inset Formula $\mathbf{b}_{1}$
\end_inset 

 and 
\begin_inset Formula $\mathbf{b}_{2}$
\end_inset 

 will be used.
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Other options of the menu allows youto choose the 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-points depending on the type of the DFT calculation to be performed:
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1
\series default 
 - the most sophisticated option, it allows one to use the point symmetry
 of the system and split the BZ into many tetrahedra for the calculation
 of the electronic DOS.
 This is specifically described in the coming Sections below
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2
\series default 
 - 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-points along a direction in the BZ can be chosen; this is useful for a
 band-structure calculation, when dispersion curves, 
\begin_inset Formula $\varepsilon_{n}(\mathbf{k})$
\end_inset 

, for each electronic band 
\begin_inset Formula $n$
\end_inset 

 are to be calculated
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\series bold 
3
\series default 
 - 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-points for a self-consistent calculation are chosen using the Monchorst-Pack
 method (either two or three integers to be given in the 2D and 3D cases,
 respectively); only inversion is assumed in this case (i.e.
 the points 
\begin_inset Formula $\mathbf{k}$
\end_inset 

 and 
\begin_inset Formula $-\mathbf{k}$
\end_inset 

 are assumed to be equivalent)