manual_3.93a.lyx

已经编译好的levoo程序

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LEV00
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 & 
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TETR
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: 
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user-friendly packages for DFT codes 
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VASP
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/
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SIESTA
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/
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CASTEP
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L.
 N.
 Kantorovich 
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This is a documentation for a package of utilities which have been written
 (initially at Keele and then continued in London at UCL and KCL) as pre-
 and post-processing tools for DFT codes working with periodic boundary
 conditions.
 At the beginning, DFT codes 
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CASTEP
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 and 
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CETEP
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were supported.
 At a later stage a complete support for the 
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VASP
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 code has also been added.
 Then, the whole structure of the two codes has been reshuffled in order
 to allow for a more flexible support for other codes and input/output formats.
 Recently, an almost complete support for the 
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SIESTA
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 code has also been added.
 
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The applications (i.e.
 offered functionality) include:
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various modifications of the system geometry (e.g.
 changing lattice vectors, breeding the system (supercells), merging geometries
 from several files of different formats (e.g.
 adding a molecule from another file to the surface), constructing a surface
 cell from a bulk one, etc.); 
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construction of molecular clusters with specific boundary conditions out
 of a bulk unit cell; 
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a powerful engine for phonons calculations (molecules and crystals); 
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calculations of the electronic Density of States (DOS), 
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plotting of charge and spin total and partial densities, calculating atomic
 charges, saving the 
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cube
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 format file for 
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gOpenMol
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 contour plotting, etc.
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an intelligent search for surface states, exploration of the (partial) electroni
c (spin) density
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and a lot more!
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Introduction
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What is this all about?
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Most of the modern condensed matter computer codes implement 
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periodic boundary conditions
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 (PBC).
 These are used not only in calculating the crystal bulk, but also for calculati
ng single molecules, surfaces, molecules adsorbed on surfaces, and so on.
 Care is needed when working in PBC, especially if complex structures are
 to be modelled, such e.g.
 as steps, kinks, dislocations.
 On the other hand, a calculation of the electronic DOS or previewing electronic
 densities require specific tools that understand PBC and the way the DFT
 codes output their data.
 
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Many workers in the field have their own little routines that do the job.
 I also started from those.
 However, I quickly realised that I cannot remember what was in each of
 the routines let along their names, input file formats, etc.
 That is why it became apparent that there is a need for a single user-friendly
 code that would do everything you might want in a way that would not require
 input files and remembering how to run it, would understand the input and
 output files of the DFT codes and would have a lot of useful features.
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Initially, I combined all my little codes into a package that included 
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-point and unit cell generator and a DOS calculator.
 At the time, only the 
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CASTEP
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 code was supported.
 As the new features being developed and new problems arose, a lot of useful
 functrionality have been added.
 Most importantly, the interface in the package codes has been completely
 rewritten to allow for different formats.
 This way support for 
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VASP
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 and 
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SIESTA
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 has been allowed and was eventually added.
 I can now say that the real purpose of the package is to accompany any
 grid based plane wave or local basis set DFT code that utilise periodic
 boundary conditions, the codes like thos ementioned above.
 
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The two most important codes in the package are 
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tetr
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 and 
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lev00
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.
 The first one is mainly to be used for
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 pre-processing
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 of the input data, e.g.
 complex modifications of your geometry input files, including the 
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-points, i.e.
 
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before
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 a DFT run.
 The second code is used for the 
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post-processing
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, i.e.
 calculating electronic DOS and charge density maps 
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after 
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the DFT run.
 As one particular application has been recently added, namely the phonon
 calculation engine, the 
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tetr
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 has gone long way beyond its initial simple pre-processing purpose and
 now does both things: it creates the necessary input files for 
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VASP
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 and 
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SIESTA
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, and then, after the calculation is performed with those codes, the 
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tetr
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 is run again to calculate the frequencies, eigenvectors and phonon DOS.
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The most sophisticated support is provided for the old 
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CASTEP/CETEP
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 code.
 These are now redundant and their support was stopped a while ago.
 Presently, 
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VASP
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 and 
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SIESTA
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 are supported only.
 Still, at the end of this manual some information on CASTEP is also provided
 (may be not working though), mainly for historical purposes.
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Menus
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The main codes 
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tetr
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 and 
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lev00
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, as well as some others, have a special tex-based interface (Text User
 Interface, TUI) that reminds menus.
 All menus work in a very simple and straightforward fashion: every menu
 item has either a number or a symbol.
 At each point in time you see on the screen the whole menu.
 
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To execute a particular option you press the number (symbol) corresponding
 to the option required paying special attention to small/capital characters
 if present, and then press Enter.
 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!
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Many menus contain several parts.
 Usually, the upper part of the menus contain the executable bits, the middle
 - some information options, while at the bottom of the menu one can find
 various options that control the other options of the menu (the settings).
 An example of a typical menu is given below (it is, in fact, the main menu
 of 
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tetr
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):
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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 \SpecialChar ~
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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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We shall be using a bold font for the menu options in what follows.
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Miscellaneous
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At the moment the package can be used on many computers where graphical
 package 
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GNUPLOT
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is available.
 Some tricks employed 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 these should be ok in Linux.
 Make files are available for Linux.
 
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I recommend to put all the source in the directory 
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\i \~{/}
TOOLS
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 in your home directory and all necessary scripts (see directory 
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SCRIPTS
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) - in your 
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\i \~{/}
bin
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 directory.
 If you have done this, the scripts may work straight away.
 
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Utility 
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tetr
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What it can do
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tetr
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 is an interactive menu-driven program which enables you: 
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can read in existing input files from 
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VASP
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, 
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SIESTA
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, old 
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CASTEP
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, 
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xyz
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 format
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can save the current geometry in the same formats
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creates a geometry file from scratch or modifies an existing geometry in
 various ways
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