Révision 9 doc/Mini_help.tex

Mini_help.tex (revision 9)
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\documentclass[a4paper,11pt]{article}
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\usepackage{a4wide}
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%\usepackage{times}
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\usepackage{graphicx}
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\usepackage[body={16cm,24.5cm}]{geometry}
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\lhead[]{}
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\rhead[]{}
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\cfoot{}
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\title{OpenPath mini-help}
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\title{Opt'n Path mini-help}
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\author{P. Fleurat-Lessard, P. Dayal \\
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Laboratoire de Chimie de l'ENS Lyon, 46 all?e d'Italie, F-69364 Lyon
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Laboratoire de Chimie de l'ENS Lyon, 46 all\'ee d'Italie, F-69364 Lyon
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Cedex 7}
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\date{Feb. 2011}
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\date{March 2013}
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\def\Path{\texttt{OpenPath}}
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\def\Path{\texttt{Opt'n Path}}
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\begin{document}
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\maketitle
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\section{introduction}
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\section{Introduction}
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\Path{} is a program that can optimize a reaction path between two
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  structures. The algorithm to optimize the path is close to the string
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  method. The originality of this program lies in the coordinate set it
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This program is an independant program that calls standard electronic
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  structure codes to get the energies and forces it needs to optimize
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  the reaction path. For now, it is coupled to Gaussian, MOPAC2009,
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  Vasp and Turbomole.
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  the reaction path. For now, it is coupled to Gaussian, MOPAC,
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  Vasp, Turbomole and Siesta.
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\section{Installation}
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We suppose here that you will install \Path{} into a directory called
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\texttt{OpenPath}. First, create the directory: 
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\texttt{optnpath}. First, create the directory: 
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\begin{verbatim}
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 mkdir OpenPath
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 cd OpenPath
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 mv ../OpenPath.tgz .
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 mkdir optnpath
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 cd optnpath
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 mv ../optnpath_x.yy.tgz .
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\end{verbatim}
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Uncompress the archive:
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\begin{verbatim}
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 gunzip OpenPath.tgz
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 tar -xvf OpenPath.tar
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 gunzip optnpath_x.yy.tgz
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 tar -xvf Optnpath.tar
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\end{verbatim}
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You should now have this \texttt{Mini\_help.pdf} file and 4 directories (doc, src, utils, examples).
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\end{verbatim}
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   Compulsory variables are: 
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\subsubsection{Compulsory variables are:}
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\begin{description}
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\item          NGeomi: Number of geometries defining the Initial path 
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\item          NGeomf: Number of geometries defining the Final path 
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\item         Nat   : Number of atoms 
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\item[NGeomi:] Number of geometries defining the Initial path 
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\item[NGeomf:] Number of geometries defining the Final path 
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\item[Nat:] Number of atoms 
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\end{description}
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          Other options 
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\subsubsection{Other options:}
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\begin{description}
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\item  Input: string that indicates the type of the input geometries.
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          Accepted values are: Cart (or Xmol or Xyz) or Vasp 
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\item    Prog: string that indicates the program that will be used for energy and gradient calculations. 
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               Accepted values are: Gaussian, Vasp or Ext. \\
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                In case of a Gaussian calculations, input must be set to Cart. 
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\item[Input:] String that indicates the type of the input geometries.
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          Accepted values are: Cart (or Xmol or Xyz), Vasp, Turbomole or Siesta.
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\item[Prog:] string that indicates the program that will be used for energy and gradient calculations. 
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               Accepted values are: Gaussian, Mopac, Vasp, Turbomole, Siesta or Ext. \\
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\begin{itemize}
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\item   In case of a Gaussian calculations, input must be set to Cart. 
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                One example of a gaussian input should be added at the end of the 
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                input file.See example file \texttt{Test\_HCN\_zmat\_g03.path}. \\
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                In the case of a VASP calculation, if input is set to Cart, then 
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              the preamble of a VASP calculation should be added at the end of 
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\item       In the case of a VASP calculation, if input is set to Cart, then 
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              the preamble of a VASP calculation s\item \texttt{Mopac}: Examples  using sequential call
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  to MOPAC2009 to calculate the energies and forces along the path.
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hould be added at the end of 
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              the input file. See example file \texttt{Test\_VASP\_cart.path}. 
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              In the case of a VASP calculation, one should also give value of the  
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              \texttt{RunMode} variable .
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\item  In the case of a SIESTA calculation, an example of a Siesta input file
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     should be added at the end of the input file. See \texttt{Test\_Siesta.path}.
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\end{itemize}
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\item RunMode: This indicates wether \Path{} should use VASP
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              routine to calculate the energy and gradient of the whole path
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\item[RunMode:] When running on a multi-processor machine, this indicates
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  wether \Path{} should calculate the energy and gradient of the whole path in parallel
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              or not. User has two options. One is to calculate the energy and
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              gradient of each point sequentially. This is usefull when
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              running on one (or two) processors. In this case,
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              in parallel with 8 or more processors, one can use VASP to
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              calculate simultaneously the energies and gradients for all
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              points, as in a normal NEB calculation. In this case,
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              \texttt{RunMode} must be set to \texttt{PARA}.
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\item ProgExe: Name (with full path) of the executable to be used to get
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              \texttt{RunMode} must be set to \texttt{PARA}. 
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 \emph{For now, this is usefull only for VASP.} \\
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\item[ProgExe:] Name (with full path) of the executable to be used to get
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  energies and gradients. For example, if VASP is used in parallel, one might
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  have something like: \\ 
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\verb!ProgExe='/usr/local/mpich/bin/mpirun -machinefile machine -np 8 ~/bin/VASP_46'!.
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Another option that I use, is to put \verb!ProgExe='./run_vasp'! and I put every option needed to run VASP
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into the \texttt{run\_vasp} file. 
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\item   PathName: Prefix used to save the path. Default is Path 
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\item   Poscar: string that will be used as the prefix for the different  
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\item[EReac:] (REAL) By default, \Path{} does not compute the energy of the reactants
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 and products. This thus indicates the reactants energy to \Path{} to have better plots
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 at the end.
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\item[EProd:] (REAL) By default, \Path{} does not compute the energy of the reactants
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 and products. This thus indicates the products energy to \Path{} to have better plots.
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\item[PathName:] Prefix used to save the path. Default is Path 
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\item[Poscar:] string that will be used as the prefix for the different  
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           POSCAR files in a VASP calculations. Usefull only if PathOnly=.TRUE., 
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           not used for internal calculations. 
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\item   IGeomRef: Index of the geometry used to construct the internal coordinates. 
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         Valid only for Coord=Zmat, Hybrid or Mixed 
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\item   Fact: REAL used to define if two atoms are linked. 
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\item[CalcName:] Prefix for the files used for the energy and gradient calculations
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\item[ISuffix:] Suffix for the input file used for energy and gradient calculations. 
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The full inputfile name will thus be \textit{CalcName}.\textit{ISuffix}.
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\item[OSuffix:] Suffix for the output file used for energy and gradient calculations.
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 The full outputfile name will thus be \textit{CalcName}.\textit{OSuffix}.
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\item[IGeomRef:] Index of the geometry used to construct the internal coordinates. 
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         Valid only for Coord=Zmat, Hybrid or Mixed.
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\item[Fact:] REAL used to define if two atoms are linked. 
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         If $d(A,B) \leq fact*(rcov(A)+rcov(B))$, then A and B are considered Linked. 
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\item   debugFile: Name of the file that indicates which subroutine should print debug info. 
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\item   Coord: System of coordinates to use. Possible choices are: 
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          - CART (or Xyz): works in cartesian 
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          - Zmat: works in internal coordinates (Zmat) 
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          - Mixed: frozen atoms, as well as atoms defined by the  
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\item[debugFile:] Name of the file that indicates which subroutine should print debug info. 
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\item[Coord:] System of coordinates to use. Possible choices are: 
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\begin{itemize}
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\item CART (or Xyz): works in cartesian 
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\item Zmat: works in internal coordinates (Zmat) 
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\item Mixed: frozen atoms, as well as atoms defined by the  
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          'cart' array(see below) are describe in CARTESIAN, whereas the 
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          others are described in Zmat  
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          - Baker: use of Baker coordinates, also called delocalized internal coordinates 
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          - Hybrid: geometries are described in zmat, but the gradient are used in cartesian 
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\item   Step\_method: method to compute the step for optimizing a geometry; choices are:  
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          - RFO: Rational function optimization 
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          - GDIIS: Geometry optimization using direct inversion in the iterative supspace 
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\item    HUpdate: method to update the hessian. By default, it is Murtagh-Sargent 
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\item  Baker: use of Baker coordinates, also called delocalized internal coordinates 
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\item Hybrid: geometries are described in zmat, but the gradient are used in cartesian 
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\end{itemize}
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\item[Step\_method:] method to compute the step for optimizing a geometry; choices are:  
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\begin{itemize}
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\item RFO: Rational function optimization 
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\item GDIIS: Geometry optimization using direct inversion in the iterative supspace 
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\end{itemize}
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\item[HUpdate:] method to update the hessian. By default, it is Murtagh-Sargent 
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         Except for geometry optimization where it is BFGS. 
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\item   MaxCyc: maximum number of iterations for the path optimization 
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\item   Smax: Maximum length of a step during path optimization 
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\item   SThresh: Step Threshold to consider that the path is stationary 
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\item   GThresh: Gradient Threshold to consider that the path is stationary, only orthogonal part is taken 
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\item   FTan: We moving the path, this gives the proportion of the displacement tangent to the path 
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\item[MaxCyc:] maximum number of iterations for the path optimization 
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\item[Smax:] Maximum length of a step during path optimization 
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\item[SThresh:] Step Threshold to consider that the path is stationary 
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\item[GThresh:] Gradient Threshold to consider that the path is stationary, only orthogonal part is taken 
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\item[FTan:] We moving the path, this gives the proportion of the displacement tangent to the path 
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         that is kept. FTan=1. corresponds to the full displacement,  
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         whereas FTan=0. gives a displacement orthogonal to the path. 
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\item   IReparam: The path is not reparameterised at each iteration. This gives the frequency of reparameterization. 
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\item   ISpline: By default, a linear interpolation is used to generate the path. 
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\item[IReparam:] The path is not reparameterised at each iteration. This gives the 
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frequency of reparameterization.  
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\item[IReparamT:] When the path is not reparameterised at each iteration, this gives the 
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frequency of reparameterization of the \emph{tangents}.
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\item[ISpline:] By default, a linear interpolation is used to generate the path. 
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            This option indicates the first step where spline interpolation is used. 
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\item[BoxTol:]  Real between 0. and 1. When doing periodic calculations, 
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        it might happen that an atom moves out of the unit cell.
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        Path detects this by comparing the displacement to boxtol:
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        if an atom moves by more than Boxtol, then it is moved back into the unit cell. Default value: 0.5.
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\item[FrozTol:]  (Real) This indicates the threshold to determine wether an atom moves between two images. Default is 1e-4.
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\item[OptGeom:] This INTEGER indicates the index of the geometry you want to optimize. 
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If \texttt{OptGeom} is set, then \Path{} performs a geometry optimization instead of a path interpolation.
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\item[GeomFile:]  Name of the file to print the geometries and their energy
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      during a geometry optimization. If this variable is not given
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      then nothing is printed.
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\item[AnaFile:]  Name of the file to print the values of the geometrical parameters
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that are monitored if \texttt{AnaGeom=.TRUE.}. Default is \textit{PathName}.dat
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\item[GplotFile:]  Name of the \texttt{gnuplot} file to plot the evolution of the geometrical parameters that are monitored if \texttt{AnaGeom=.TRUE.}. Default is \textit{PathName}.gplot
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%% Not described here: NMaxPtPath, NGintMax (too technical ?)
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\end{description}
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          Arrays: 
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\subsubsection{Arrays:}
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\begin{description}
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\item   Rcov: Array containing the covalent radii of the first 80 elements. 
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\item[Rcov:] Array containing the covalent radii of the first 86 elements. 
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         You can modify it using, \verb!rcov(6)=0.8!. 
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\item   Mass: Array containing the atomic mass of the first 80 elements. 
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\item   AtTypes: Name of the different atoms used in a VASP calculations. 
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\item[Mass:] Array containing the atomic mass of the first 86 elements. 
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\item[AtTypes:] Name of the different atoms used in a VASP calculations. 
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          If not given, Path will read the POTCAR file. 
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\end{description}
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          Flags: 
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\subsubsection{Flags:}
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\begin{description}
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\item        MW:  Flag. True if one wants to work in Mass Weighted coordinates. Default=.TRUE. 
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\item       Renum: Flag. True if one wants to reoder the atoms in the
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  initial order. default is .TRUE. most of the time.  
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\item       OptProd: True if one wants to optimize the geometry of the products. 
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\item       OptReac: True if one wants to optimize the geometry of the reactants. 
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\item       CalcEProd: if TRUE the product energy will be
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  computed. Default is FALSE. Not Compatible with RunMode=Para". 
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\item       CalcEReac: if TRUE the reactants energy will be
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  computed. Default is FALSE. Not Compatible with RunMode=Para". 
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\item       PathOnly:TRUE if one wants to generate the initial path, and stops.  
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\item       Hinv: if True, then Hessian inversed is used. 
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\item       IniHup: if True, then Hessian inverse is extrapolated
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\item[MW:]  Flag. True if one wants to work in Mass Weighted coordinates. Default=.TRUE. 
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\item[Renum:] Flag. True if one wants to reoder the atoms in the
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  initial order. default is .TRUE. unless for \texttt{Coord} equals \texttt{CART}.
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\item[OptProd:] True if one wants to optimize the geometry of the products. 
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\item[OptReac:] True if one wants to optimize the geometry of the reactants. 
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\item[CalcEProd:] if TRUE the product energy will be
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  computed. Default is FALSE. Not Compatible with \texttt{RunMode=Para}. 
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\item[CalcEReac:] if TRUE the reactants energy will be
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  computed. Default is FALSE. Not Compatible with \texttt{RunMode=Para}. 
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\item[PathOnly:] TRUE if one wants to generate the initial path, and stops.  
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\item[Align:] If .FALSE., successive geometries along the path are not aligned on each other before path interpolation. Default is .TRUE. if there are 4 atoms or more.
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\item[Hinv:] if True, then Hessian inversed is used. 
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\item[IniHup:] if True, then Hessian inverse is extrapolated
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  using the initial path calculations.  
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\item       HupNeighbour: if True, then Hessian inverse is
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\item[HupNeighbour:]  if True, then Hessian inverse is
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  extrapolated using the neighbouring points of the path.  
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\item       FFrozen: True if one wants to freeze the positions of some atoms.  
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\item[FFrozen:] True if one wants to freeze the positions of some atoms.  
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                If True, a \verb!&frozenlist! namelist containing the
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                list of frozen atoms must be given.  
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                 If VASP is used, and frozen is not given 
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        here, the program will use the F flags of the input geometry 
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\item       FCart:  True if one wants to describe some atoms using cartesian coordinates.  
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\item[FCart:]  True if one wants to describe some atoms using cartesian coordinates.  
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               *** Only used in 'mixed' calculations. *** 
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             If True, a \verb!&cartlist! namelist containing the list of cart atoms must be given. 
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             By default, only frozen atoms are described in cartesian coordinates. 
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\item       Autocart: True if you want to let the program choosing the cartesian atoms. 
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\item       VMD: TRUE if you want to use VMD to look at the Path. Used only for VASP for now 
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\item[Autocart:] True if you want to let the program choosing the cartesian atoms. 
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\item[VMD:] TRUE if you want to use VMD to look at the Path. Used only for VASP for now.
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\item[WriteVASP:] TRUE if you want to print the images coordinates in POSCAR files.
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See also the POSCAR option. This can be used only if prog or input=VASP.
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\item[AnaGeom:] If TRUE, Opt'n Path will create a file .dat for geometries analysis.
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        If True, Opt'n Path will look for the AnaList namelist after the Path Namelist.
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\item[DynMaxStep:] if TRUE, the maximum allowed step is updated at each step, for each geometry.
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        If energy goes up, $Smax=Smax*0.8$, if not $Smax=Smax*1.2$. 
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       It is ensured that the dynamical Smax is within $[0.5*SMax_0,2*Smax_0]$.
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\end{description}
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\subsubsection{Additional namelists:}
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\begin{description}
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\item[\&cartlist list= \ldots{} \&end] This gives the list of atoms that are described using cartesian coordinates. Read only if \texttt{FCart=.TRUE.}. To indicate an atom range, from 1 to 5 for example, one can put 1 -5 in the list. For example: \\
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\texttt{\&cartlist list = 1 2 6 12 -20 \&end} \\
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will described atoms 1, 2, 6, 12, 13, 14, 15, 16, 17, 18, 19 and 20 in cartesian.
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\item[\&Frozenlist list= \ldots{}  \&end] This gives the list of atoms that are frozen during optimization. Read only if \texttt{FFrozen=.TRUE.}. To indicate an atom range, from 1 to 5 for example, one can put 1 -5 in the list. 
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\item[\&Analist nb= \ldots{} \&end] list of variables for geometry analysis. If present and if AnaGeom=T then
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     Opt'n Path will read it and print the values of the variable in a .dat file
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    If AnaGeom is T but Analist is not given, then Path.dat just contains the energy. 
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Analist contains the number of variables to monitor: Nb, and is followed by the description
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of the variables among:
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b(ond) At1 At2
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a(ngle) At1 At2 At3
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d(ihedral) At1 At2 At3 At4
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c NbAt At1 At2 At3 At4 At5... to create a center of mass. The centers of mass are added
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at the end of the real atoms of the system.
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\end{description}
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\subsection{Examples}
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More to come...      have a look at the files provided in the
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\texttt{examples} directory. In particular, you will find there three
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directories containing easy-to-use examples. That is, each directory contains
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\end{itemize}
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\end{itemize}
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\item \texttt{Mopac}: Examples  using sequential call
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  to MOPAC2009 to calculate the energies and forces along the path.
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  to MOPAC to calculate the energies and forces along the path.
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\item \texttt{Siesta}: Examples  using sequential call
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  to Siesta to calculate the energies and forces along the path.
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\item \texttt{Test}: Examples  using the analytical HCN potential
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  energy surface to calculate the energies and forces along the path.
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As this is fast, we also provide other Analysis tools.

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