manual_3.93a.lyx

已经编译好的levoo程序

, where each time you change your system, the symmetry group is recalculated
 so that you can check the symmetry at every stage (option 
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Sy
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).
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In order to do a band-structure calculation, you should first relax your
 system and obtain the electronic density.
 Note that the ground state density can be left unchanged if you just 
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rotate
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 your coordinate system (we assume that it is written with respect to the
 fractional coordinates of the grid points in your cell; this supposed to
 be the case in both 
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VASP
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 and 
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SIESTA
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).
 However, if you have to 
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shift
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 your system by some vector, then the density matrix should be recalculated
 and a new file must be produced.
 This option is provided by the utility 
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lev00
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 (see Section 
\begin_inset LatexCommand \ref{sub:Ro-shifted-system-lev00}

\end_inset 

).
 Therefore, it is always wise to think about it 
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before
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 running the ground state calculation: choose the most symmetrical orientation
 of the system with respect to the Cartesian axes, use 
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\emph on 
tetr
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\emph default 
 to show the point group every time!
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Main menu
\begin_inset LatexCommand \label{sec:Main-menu-tetr}

\end_inset 


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The main menu looks like this: 
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/---------------------------------------------------
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|....................
 MAIN MENU:.....................|
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---------------------------------------------------/
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>>>>>>>>>>>>> Create unit cell from scratch <<<<<<<<
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[current geometry will be lost] 
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B.
 Generate supercell geometry from scratch
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>>>>>>>>>>>>>>>>> Cluster construction <<<<<<<<<<<<
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Cl.
 Build up a cluster from the lattice
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>>>>>>>>>>>>> Geometry file already exists <<<<<<<<<<
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M.
 Complex cell modifications
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KP.
 k-points generation 
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>>>>>>>>>>>>>>>>> Coulomb potential <<<<<<<<<<<<<<<
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Ew.
 Coulomb potential inside the unit cell
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>>>>>>>>>>>>>>> Calculation of phonons <<<<<<<<<<<<<
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Vm.
 Vibrations of molecules => preparation
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Vc.
 Vibrations of crystals (point group) => preparation
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Vs.
 Vibrations of crystals (space group) => preparation
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V2.
 Vibrations => calculation [normal modes]
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V3.
 Vibrations => application [DOS, masses]
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>>>>>>>>>>>> Representation/visualisation <<<<<<<<<<<
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Cm.
 Compare geometry with the one in another file
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D.
 Distances between atoms
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Ch.
 Check specified point in the cell
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Sb.
 Save in a box running across adjacent cells
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>>>>>>>>>>>>>> Potential energy surface <<<<<<<<<<<<<
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Mv.
 PES: move atoms keeping the symmetry
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---------- g e n e r a l s e t t i n g s -----------
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XY.
 Format of <geom.xyz> is set to Xmol
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R.
 Read geometry from another file
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S.
 Save
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Q.
 Quit.
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Specify the character and press ENTER ------->
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The sections below explain all these options in some detail.
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B - Generate supercell geometry from scratch
\begin_inset LatexCommand \label{sub:B-option-tetr}

\end_inset 


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One can generate lattice vectors of the cell and atomic positions inside
 the cell from scratch.
 The initial 
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B-option
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 menu is this:
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========= CHOOSE AN OPTION:
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1.
 Number of species: <===== undefined
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3.
 Basic translations of the PRIMITIVE CELL <===== undefined
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-------------- Extention matrix {cell -> supercell} -----------
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5.
 Specify directly
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| 1 0 0 |
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IJ(i,j)= | 0 1 0 |, ext= 1
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| 0 0 1 |
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-------------- g e n e r a l s e t t i n g s ----------------
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Or.
 Move atoms closer to origin: NO
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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: <Angstroms> 
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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= 0
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Q.
 Quit: return to the previous setting (if exists)
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----------> Choose an appropriate option:
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You must first specify all the data in 
\begin_inset Quotes eld
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undefined
\begin_inset Quotes erd
\end_inset 

 fields.
 Start from the option 1 and specify the primitive unit cell information.
 New options will appear that require additional information.
 The primitive lattice vectors 
\begin_inset Formula $\mathbf{a}_{1},\mathbf{a}_{2},\mathbf{a}_{3}$
\end_inset 

are specified either manually or from the list, both to be found in the
 following menu:
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--------------------------------------------------
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--------- Choose one Bravais lattices: -----------
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--------------------------------------------------
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0.Manually
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1.Triclinic system
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2.Monoclinic system.
 Simple lattice
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3.Monoclinic system.
 Side-centered lattice
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4.Orthorhombic system.
 Simple lattice
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5.Orthorhombic system.
 Fcc-1 lattice
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6.Orthorhombic system.
 Fcc-2 lattice
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7.Orthorhombic system.
 Bcc lattice
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8.Tetragonal system.
 Simple lattice
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9.Tetragonal system.
 Bcc-1 lattice
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10.Tetragonal system.
 Bcc-2 lattice (diff.setting)
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11.Cubic system.
 Simple lattice
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12.Cubic system.
 Bcc lattice
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13.Cubic system.
 Fcc lattice
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14.Rhombohedral system.
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15.Hexagonal system
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-------> Choose the appropriate number ------->
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The cell you want to construct may consist of several primitive cells with
 lattice vectors 
\begin_inset Formula \begin{equation}
\mathbf{A}_{i}=\sum_{j=1}^{3}T_{ij}\mathbf{a}_{j}\label{eq:a-to-A}\end{equation}

\end_inset 

where 
\begin_inset Formula $\mathbf{T}$
\end_inset 

 is the 
\begin_inset Formula $3\times3$
\end_inset 

 transformation (extention) matrix consisting only of integer numbers.
 By default, the extention matrix is the unit matrix, i.e.
 
\begin_inset Formula $\mathbf{A}_{i}=\mathbf{a}_{i}$
\end_inset 

.
 However, using options 
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4
\series default 
 or
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 5
\series default 
 from the B-option menu, the matrix 
\begin_inset Formula $\mathbf{T}$
\end_inset 

 can be specified either directly (option 
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4
\series default 
) or by specifying the vectors 
\begin_inset Formula $\mathbf{A}_{i}$
\end_inset 

(option 
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5
\series default 
).
 In the latter case the matrix 
\begin_inset Formula $\mathbf{T}$
\end_inset 

 is calculated and it is checked if it consists of integers only.
 
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Finally, the unit cell is generated in option 
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7
\series default 
.
 If you leave the B-option menu by pressing 
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Q
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 (and Enter), the main menu of 
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tetr
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\emph default 
 will appear, so that you can modify your setting, add 
\begin_inset Formula $\mathbf{k}$
\end_inset 

-points and then save them in the format of your choice.
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Cl - Build up a cluster from the lattice
\begin_inset LatexCommand \label{sub:Cl-option-tetr}

\end_inset 


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This option becomes available in the main menu if the geometry is known,
 i.e.
 it has either been read in or constructed from scratch.
 The idea is this: starting from one atom, build up all or some its nearest
 neighbours, then nearest neighbours to latter atoms and so on.
 Finally, if desired, some or all boundary atoms of the cluster are terminated
 by hydrogen atoms positioned at a certain distance from them and along
 the directions of the actual bonds of the bulk system.
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The 
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Cl-menu
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 initially looks like this:
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>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<
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...
 CURRENT lattice vectors for the supercell ARE...
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AJ(1): 10.88160 0.00000 0.00000
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AJ(2): 0.00000 10.88160 0.00000
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AJ(3): 0.00000 0.00000 10.88160
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