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\documentclass[a4paper,11pt]{article}
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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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\usepackage[latin1]{inputenc}
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\usepackage[T1]{fontenc}
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\usepackage{ae,aecompl}
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%\input{m-pictex.tex}
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%\usepackage{m-ch-en}
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\usepackage{amsmath,amssymb}
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%\usepackage{slashbox}
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%\usepackage{psfrag}
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%\usepackage{multirow}
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%\usepackage{amscd}
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%\usepackage{empheq}
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%\usepackage{yhmath}
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%\usepackage{array}
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\usepackage{fancyhdr}
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%\usepackage{braket}
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\usepackage{marvosym}
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%\usepackage{xr}
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\DeclareGraphicsExtensions{.eps,.ps}
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\graphicspath{{.}{../}}
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\renewcommand{\arraystretch}{1.2}
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\setcounter{tocdepth}{2}
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\makeatletter
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\@addtoreset{section}{part}
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\makeatother
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\lhead[]{}
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\rhead[]{}
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\cfoot{}
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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\'ee d'Italie, F-69364 Lyon
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Cedex 7}
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\date{March 2013}
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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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\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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 can use to generate and optimize the path.
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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, 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{optnpath}. First, create the directory:
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\begin{verbatim}
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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 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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\section{Compilation}
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Go to the directory  in which you have uncompressed the files.
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Change to the \texttt{src} directory.
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Edit the \texttt{Makefile} to change the \texttt{Machine} description
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according to the compiler you want to use. Main choices are:
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gfortran, g95, ifort, pgf, xlf and pathscale for now. You might also
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have to check that the locations of
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the libraries are ok.
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Type \texttt{make}. You should now have a file called
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\texttt{Path.exe} in this directory, as well as two utilities called
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\texttt{xyz2scan} and \texttt{xyz2path} located in the \texttt{utils}
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directories. You should copy all these executables to your
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\texttt{~/bin} directory (or any place from which they can be executed).
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\section{Use}
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\subsection{Path calculation}
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 To call \Path{}, you can type:
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\verb=Path.exe Input_file Output_file=
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The input file \texttt{Input\_file} is based on a namelist and looks like:
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\begin{verbatim}
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 &path
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 nat=3, ! Number of atoms
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 ngeomi=3, ! Number of initial geometries
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 ngeomf=12, !Number of geometries along the path
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 OptReac=.T., ! Do you want to optimize the reactants ?
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 OptProd=.T., ! Optimize the products
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 coord='zmat', ! We use Z-matrix coordinates
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 maxcyc=31, ! Max number of iterations
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 IReparam=2,! re-distribution of points along the path every 2 iterations
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 ISpline=50, ! Start using spline interpolation at iteration 50
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 Hinv=.T. , ! Use inverse of the Hessian internally (default: T)
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 MW=T, ! Works in Mass Weighted coordiante (default T)
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 PathName='Path_HCN_zmat_test', ! Name of the file used for path outputs
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 prog='gaussian',! we use G03 to get energy and gradients
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 SMax=0.1 ! Displacement cannot exceed 0.1 atomic units (or mass weighted at. unit)
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 /
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  3
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 Energy :      0.04937364
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 H     0.0000     0.0000     0.0340
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 C     0.0000     0.0000     1.1030
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 N     0.0000     0.0000     2.2631
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  3
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 Energy :      0.04937364
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 H     0.0000     1.1000     1.1030
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 C     0.0000     0.0000     1.1030
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 N     0.0000     0.0000     2.2631
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3
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 CNH
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H 0.000000    0.000000    3.3
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C 0.000000    0.000000    1.1
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N 0.000000    0.000000    2.26
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%chk=Test
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#P  AM1 FORCE
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 HCN est bien
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0,1
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H 0.000000    0.000000    0.000000
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C 0.000000    0.000000    1.000
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N 0.000000    0.000000    3.00
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\end{verbatim}
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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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\end{description}
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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), 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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\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:] 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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              \texttt{RunMode} should be put to \texttt{SERIAL}.When running
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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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 \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[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[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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\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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\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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         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
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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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\subsubsection{Arrays:}
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\begin{description}
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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 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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\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. 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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  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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                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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               *** 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[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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all the files you need to launch the application. For now, you have working
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examples for:
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\begin{enumerate}
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\item \texttt{Gaussian}: Examples  using sequential call
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  to Gaussian to calculate the energies and forces along the path.
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\item \texttt{VASP}: Examples  using
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  to VASP to calculate the energies and forces along the path.
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As VASP can perform NEB calculations, Path can use it in two ways:
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Serial or Parallel.
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\begin{itemize}
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\item[Serial]
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In the Serial mode, Path uses Vasp to compute the energy and forces of
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each image separately (as it does for Gaussian for example).
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Therefore, the INCAR file should not contain any references to the
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number of images (no IMAGES command!).
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\item[Parallel]
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In the Parallel mode, Path uses VASP to compute at once the energies
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and forces for all the images (as VASP does for a NEB calculation).
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Therefore, the INCAR file MUST contain the IMAGES command.
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More, the directories 00, 01, ... should exist.
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\item[Home or Scratch ?]
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On our local cluster, it is adviced to perform the calculations on the
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/scratch directory that is local rather than on the /home that is
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mounted  via NFS and is thus slow.
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However, when doing so, we sometimes had troubles with VASP, and
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discovered that all files should be copied on the /scratch of all
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machines.
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Therefore, the scripts are a bit tricky.
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In case your computer center is similar to ours, we provide 2 SGE
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scripts:
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\begin{itemize}
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\item[run\_Path\_SGE\_home] performs the VASP calculations in the /home
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directory
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\item[run\_Path\_SGE\_scratch] creates the directories, copies the
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  files and performs the VASP calculations in the local /scratch
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  directories.
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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 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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See README files in the Cart and Zmat subdirectories.
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\end{enumerate}
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\subsection{Path analysis}
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In order to analyse the path evolution, we provide some utilities, in
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the \texttt{utils} directory. \texttt{xyz2scan} and \texttt{xyz2path}
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have to be compiled. For this, go to either the \texttt{src} or the
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\texttt{utils} directory and type \texttt{make utils}.
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Here is a brief description of these utilities.
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\begin{itemize}
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\item \texttt{AnaPath} and/or \texttt{AnaPathref} \\
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These scripts analyse a calculated path. They use \texttt{xyz2path} to
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convert the cartesian coordinates saved by \Path{} into a data file
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(called PathName.datl) that be plotted using the gnuplot files that are
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also created. They all plot the path energy  but in different ways:
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\begin{itemize}
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\item[PathName\_l.gplot] plots the energy of the first iteration (the
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  initial path) together with the energy of the following iterations,
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  but one at a time.
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\item[PathName\_l2.gplot]  plots the energy of the path for all
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  iterations, with respect to the
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curvilinear distance along the path.
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\item[PathName\_l3.gplot]  plots the energy of the path for all
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  iterations, with respect to the index of the images.
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\end{itemize}
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\item \texttt{xyz2path} and \texttt{xyz2scan} convert a bunch of
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  cartesian coordinates into
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  a data file. They are very similar: the only difference is the way
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  they print their results. For \texttt{xyz2scan} the analyses are
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  indiced using the geometry number whereas \texttt{xyz2path} computes
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  the mass weighted distance between two geometries and uses this
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  distance to index the results. \\
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They both use a file called 'list' to perform the analysis,  which has
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the following structure:  each line contains the type of the value you
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want to follow, it can be:
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\begin{itemize}
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\item[b]  for a Bond distance
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\item[a] for an angle
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\item[d] for a dihedral
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\item[c] to create a center of mass
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\end{itemize}
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This descriptor is followed by the number of the atoms involved.  The
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exception, is the \texttt{c} command that is followed by the number of
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atoms used to define this center of mass, and then the index of the atoms.
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A typical file can be:
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\begin{verbatim}
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 b  1  2
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 b 2  3
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 a 1 2 3
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 c  2 1 2   <- create a new atom located at the middle of the 1-2 bond.
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\end{verbatim}
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The cartesian geometries have to follow the XMol format. If the
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comment line contains \texttt{E=} then \texttt{xyz2scan} and
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\texttt{xyz2path} will read the following number and take it as the
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image energy.
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\end{itemize}
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\end{document}