manual_3.93a.lyx

已经编译好的levoo程序

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>>>>>>>>>>>>>>>> Current species are: <<<<<<<<<<<<<<
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Si O
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========= CHOOSE AN OPTION:
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/================================================
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|| HELP: when using options N and H, you may not ||
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|| be bothered about internal cluster atoms as ||
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|| those will be ignored anyway ||
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================================================/
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R.
 Read existing cluster geometry
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1.
 START HERE: choose the first cluster atom
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-------------- g e n e r a l s e t t i n g s ----------------
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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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Co.
 Show lattice atomic positions
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Hd.
 Distance between an atom and H is: 1.00000000000000 
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Nd.
 Spherical belt width when finding nn is: 0.100000001490116 
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W.
 Write <geom.xyz> file for the current cluster
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Q.
 Proceed/Quit
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----------> Choose an appropriate option:
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At the top, lattice vectors of the unit cell are shown together with existing
 species.
 Start from option 
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1
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 that will prompt you to choose the very first atom of the cluster.
 After this is done, the menu grows into: 
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R.
 Read existing cluster geometry
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1.
 Cluster has been started from atom = 1
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Species = Si
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Position = ( 0.05194, 0.05194, 0.03418)
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N.
 Build all first neighbours around atom(s)
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H.
 Terminate a range of atoms with hydrogens
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mH.
 Move a range of H atoms along bonds
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5.
 Rename a range of atoms: change species
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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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---------------------- shift ---------------------------------
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O.
 General shift of the cluster (new origin)
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Cm.
 Shift the cluster to the centre of mass
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------------------------- final options ----------------------
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Rt.
 Rotate the WHOLE cluster about the X,Y,Z axes
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Mv.
 Move atom(s)
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-------------- g e n e r a l s e t t i n g s ----------------
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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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Co.
 Show lattice atomic positions
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Hd.
 Distance between an atom and H is: 1.00000000000000 
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Nd.
 Spherical belt width when finding nn is: 0.100000001490116 
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W.
 Write <geom.xyz> file for the current cluster
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Cc.
 Show current atomic positions in Cartesian
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S.
 Save geometry
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Q.
 Proceed/Quit
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----------> Choose an appropriate option:
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Now it is possible to choose the first shell of nearest neighbours of the
 first atom by pressing 
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N
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.
 All nearest neighbours of the first atom will be added.
 This is decided within a certain thickness specified in settings by 
\series bold 
Nd
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.
 Two new options appear in the Cl-menu: 
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/3.
 Remove a range of atoms from the cluster 
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4.
 Keep a range of atoms in the cluster: remove the rest 
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that allow you to remove unwanted atoms from the cluster.
 Next time 
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N
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 is chosen, you will be prompted to give numbers of atoms around which the
 nearest neighbours are to be constructed.
 This process can be continued almost indefinitely and leads to a cluster
 of atoms that is a fragment of the bulk crystal.
 
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At the end of the construction, by pressing option 
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H
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, it is possible to terminate some or all atoms with hydrogens.
 Their distance from the boundary cluster atoms is determined by 
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Hd
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 in the settings.
 If the distance appeared wrong, you can either undo this step (option 
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U
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), change the setting (option 
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Nd
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) and then repeat the construction.
 Alternatively, the atom-H distances can be corrected using option 
\series bold 
mH
\series default 
.
 
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Note that, when specifying a range of atoms (options 
\series bold 
N
\series default 
 and 
\series bold 
H
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), it is possible to include internal atoms of the cluster as well in the
 lists; this is very convenient and does not have any effect at all as only
 external atoms will be considered anyway.
 
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At each step, the current arrangement of the cluster atoms can be seen in
 
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Cc
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.
 If the option 
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XY
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 is on (either at 
\series bold 
\emph on 
Xmol
\series default 
\emph default 
 or 
\series bold 
\emph on 
Ymol
\series default 
\emph default 
), then you can preview the cluster by invoking 
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\emph on 
Xmol
\series default 
\emph default 
 or similar software and reading in the file 
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geom.xyz
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.
 This file is dumped automatically in the current directory every time a
 change is made.
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Additionally to the above mentioned options, it is also possible to change
 species (or 
\begin_inset Quotes eld
\end_inset 

rename
\begin_inset Quotes erd
\end_inset 

) a set of atoms (option 
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5
\series default 
).
 The option 
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T
\series default 
 allows a different (and, in many cases, more convenient) way of choosing
 atoms 
\begin_inset Quotes eld
\end_inset 

by lists
\begin_inset Quotes erd
\end_inset 

 (Section 
\begin_inset LatexCommand \ref{sec:Menus}

\end_inset 

).
 At any point the cluster can be shifted as a whole (options 
\series bold 
O
\series default 
 and 
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Cm
\series default 
).
 
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At the end of the construction some or all atoms can be moved to new positions,
 option 
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Mv
\series default 
, seen Section 
\begin_inset LatexCommand \ref{sub:Mv--Move-atoms}

\end_inset 

.
 Finally, the 
\emph on 
whole
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 system can be rotated (option 
\series bold 
Rt
\series default 
, see Section 
\begin_inset LatexCommand \ref{sub:Rt-Rotate-atoms}

\end_inset 

).
 Note that either of the options 
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Mv
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 and 
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Rt
\series default 
 has been used, it will not longer be possible to add more atoms to the
 system and/or terminate boundary atoms with hydrogens, i.e.
 options 
\series bold 
N
\series default 
 and 
\series bold 
H
\series default 
 will be disabled (unvisible).
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Finally, the cluster geometry can be saved in either an 
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xyz
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 or a 
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mol
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 file formats, the latter is an internal format of the 
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Cl
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 option.
 Files in the 
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mol
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 format can be read in by the option 
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R
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 of the Cl-menu (e.g.
 from the previous unfinished project).
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M - Complex cell modifications
\begin_inset LatexCommand \label{sub:M-option-tetr}

\end_inset 


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An extremely powerful option! It allows you to modify your existing geometry
 in a number of ways and build up your final periodic cell.
 You will be given an extended menu with self-explanatory options.
 You should be able to change your lattice vectors; extend your cell; rotate,
 shift the system; add, remove, shift atoms; change their species; construct
 a slab for the surface calculation using e.g.
 Millers indices, etc.
 What is more, after every step a 
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geom.xyz
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 (xyz-format) file with the system geometry is written in the current directory
 so that you can preview your cell on the fly as you build it using a molecular
 viewer (e.g.
 
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\emph on 
Xmol
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\emph default 
)! In fact, you can even preview it as an extended cell (the option 
\series bold 
Bb
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).
 Every step can also be undone.
 
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The M-menu 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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>>>>>>>>>>>>>>>> Current species are: <<<<<<<<<<<<<<
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Si O
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========= CHOOSE AN OPTION:
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/==================================================
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|| HELP: a complex transformation is obtained by ||
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|| applying elementary operations one after another||
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==================================================/
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1.
 General shift of the system (new origin)
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2.
 Shift the system to the center of mass
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3.
 Rotate the system (the same origin)
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4.
 Move an atom to an equivalent position
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Rf.
 Choose equivalent positions wrt reference input file
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44.