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 1 2 3 1 pfleura2 \documentclass[a4paper,11pt]{article}  1 pfleura2 %\usepackage{times}  1 pfleura2 \usepackage{graphicx}  1 pfleura2 \usepackage[body={16cm,24.5cm}]{geometry}  1 pfleura2 \usepackage[latin1]{inputenc}  1 pfleura2 \usepackage[T1]{fontenc}  1 pfleura2 \usepackage{ae,aecompl}  1 pfleura2 %\input{m-pictex.tex}  1 pfleura2 %\usepackage{m-ch-en}  1 pfleura2 \usepackage{amsmath,amssymb}  1 pfleura2 %\usepackage{slashbox}  1 pfleura2 %\usepackage{psfrag}  1 pfleura2 %\usepackage{multirow}  1 pfleura2 %\usepackage{amscd}  1 pfleura2 %\usepackage{empheq}  1 pfleura2 %\usepackage{yhmath}  1 pfleura2 %\usepackage{array}  1 pfleura2 \usepackage{fancyhdr}  1 pfleura2 %\usepackage{braket}  1 pfleura2 \usepackage{marvosym}  1 pfleura2 %\usepackage{xr}  1 pfleura2 1 pfleura2 1 pfleura2 \DeclareGraphicsExtensions{.eps,.ps}  1 pfleura2 \graphicspath{{.}{../}}  1 pfleura2 1 pfleura2 \renewcommand{\arraystretch}{1.2}  1 pfleura2 \setcounter{tocdepth}{2}  1 pfleura2 \makeatletter  1 pfleura2 \@addtoreset{section}{part}  1 pfleura2 \makeatother  1 pfleura2 1 pfleura2 \lhead[]{}  1 pfleura2 \rhead[]{}  1 pfleura2 \cfoot{}  9 pfleura2 \title{Opt'n Path mini-help}  1 pfleura2 \author{P. Fleurat-Lessard, P. Dayal \\  9 pfleura2 Laboratoire de Chimie de l'ENS Lyon, 46 all\'ee d'Italie, F-69364 Lyon  1 pfleura2 Cedex 7}  9 pfleura2 \date{March 2013}  1 pfleura2 9 pfleura2 \def\Path{\texttt{Opt'n Path}}  1 pfleura2 \begin{document}  1 pfleura2 \maketitle  1 pfleura2 9 pfleura2 \section{Introduction}  1 pfleura2 \Path{} is a program that can optimize a reaction path between two  1 pfleura2  structures. The algorithm to optimize the path is close to the string  1 pfleura2  method. The originality of this program lies in the coordinate set it  1 pfleura2  can use to generate and optimize the path.  1 pfleura2 1 pfleura2 This program is an independant program that calls standard electronic  1 pfleura2  structure codes to get the energies and forces it needs to optimize  9 pfleura2  the reaction path. For now, it is coupled to Gaussian, MOPAC,  9 pfleura2  Vasp, Turbomole and Siesta.  1 pfleura2 1 pfleura2 \section{Installation}  1 pfleura2 We suppose here that you will install \Path{} into a directory called  9 pfleura2 \texttt{optnpath}. First, create the directory:  1 pfleura2 \begin{verbatim}  9 pfleura2  mkdir optnpath  9 pfleura2  cd optnpath  9 pfleura2  mv ../optnpath_x.yy.tgz .  1 pfleura2 \end{verbatim}  1 pfleura2 Uncompress the archive:  1 pfleura2 \begin{verbatim}  9 pfleura2  gunzip optnpath_x.yy.tgz  9 pfleura2  tar -xvf Optnpath.tar  1 pfleura2 \end{verbatim}  1 pfleura2 You should now have this \texttt{Mini\_help.pdf} file and 4 directories (doc, src, utils, examples).  1 pfleura2 1 pfleura2 \section{Compilation}  1 pfleura2 Go to the directory in which you have uncompressed the files.  1 pfleura2 Change to the \texttt{src} directory.  1 pfleura2 Edit the \texttt{Makefile} to change the \texttt{Machine} description  1 pfleura2 according to the compiler you want to use. Main choices are:  1 pfleura2 gfortran, g95, ifort, pgf, xlf and pathscale for now. You might also  1 pfleura2 have to check that the locations of  1 pfleura2 the libraries are ok.  1 pfleura2 Type \texttt{make}. You should now have a file called  1 pfleura2 \texttt{Path.exe} in this directory, as well as two utilities called  1 pfleura2 \texttt{xyz2scan} and \texttt{xyz2path} located in the \texttt{utils}  1 pfleura2 directories. You should copy all these executables to your  1 pfleura2 \texttt{~/bin} directory (or any place from which they can be executed).  1 pfleura2 1 pfleura2 \section{Use}  1 pfleura2 \subsection{Path calculation}  1 pfleura2  To call \Path{}, you can type:  1 pfleura2 \verb=Path.exe Input_file Output_file=  1 pfleura2 The input file \texttt{Input\_file} is based on a namelist and looks like:  1 pfleura2 \begin{verbatim}  1 pfleura2  &path  1 pfleura2  nat=3, ! Number of atoms  1 pfleura2  ngeomi=3, ! Number of initial geometries  1 pfleura2  ngeomf=12, !Number of geometries along the path  1 pfleura2  OptReac=.T., ! Do you want to optimize the reactants ?  1 pfleura2  OptProd=.T., ! Optimize the products  1 pfleura2  coord='zmat', ! We use Z-matrix coordinates  1 pfleura2  maxcyc=31, ! Max number of iterations  1 pfleura2  IReparam=2,! re-distribution of points along the path every 2 iterations  1 pfleura2  ISpline=50, ! Start using spline interpolation at iteration 50  1 pfleura2  Hinv=.T. , ! Use inverse of the Hessian internally (default: T)  1 pfleura2  MW=T, ! Works in Mass Weighted coordiante (default T)  1 pfleura2  PathName='Path_HCN_zmat_test', ! Name of the file used for path outputs  1 pfleura2  prog='gaussian',! we use G03 to get energy and gradients  1 pfleura2  SMax=0.1 ! Displacement cannot exceed 0.1 atomic units (or mass weighted at. unit)  1 pfleura2  /  1 pfleura2  3  1 pfleura2  Energy : 0.04937364  1 pfleura2  H 0.0000 0.0000 0.0340  1 pfleura2  C 0.0000 0.0000 1.1030  1 pfleura2  N 0.0000 0.0000 2.2631  1 pfleura2  3  1 pfleura2  Energy : 0.04937364  1 pfleura2  H 0.0000 1.1000 1.1030  1 pfleura2  C 0.0000 0.0000 1.1030  1 pfleura2  N 0.0000 0.0000 2.2631  1 pfleura2 3  1 pfleura2  CNH  1 pfleura2 H 0.000000 0.000000 3.3  1 pfleura2 C 0.000000 0.000000 1.1  1 pfleura2 N 0.000000 0.000000 2.26  1 pfleura2 %chk=Test  1 pfleura2 #P AM1 FORCE  1 pfleura2 1 pfleura2  HCN est bien  1 pfleura2 1 pfleura2 0,1  1 pfleura2 H 0.000000 0.000000 0.000000  1 pfleura2 C 0.000000 0.000000 1.000  1 pfleura2 N 0.000000 0.000000 3.00  1 pfleura2 1 pfleura2 \end{verbatim}  1 pfleura2 9 pfleura2 \subsubsection{Compulsory variables are:}  1 pfleura2 \begin{description}  9 pfleura2 \item[NGeomi:] Number of geometries defining the Initial path  9 pfleura2 \item[NGeomf:] Number of geometries defining the Final path  9 pfleura2 \item[Nat:] Number of atoms  1 pfleura2 \end{description}  9 pfleura2 9 pfleura2 9 pfleura2 \subsubsection{Other options:}  1 pfleura2 \begin{description}  9 pfleura2 \item[Input:] String that indicates the type of the input geometries.  9 pfleura2  Accepted values are: Cart (or Xmol or Xyz), Vasp, Turbomole or Siesta.  9 pfleura2 \item[Prog:] string that indicates the program that will be used for energy and gradient calculations.  9 pfleura2  Accepted values are: Gaussian, Mopac, Vasp, Turbomole, Siesta or Ext. \\  9 pfleura2 \begin{itemize}  9 pfleura2 \item In case of a Gaussian calculations, input must be set to Cart.  1 pfleura2  One example of a gaussian input should be added at the end of the  1 pfleura2  input file.See example file \texttt{Test\_HCN\_zmat\_g03.path}. \\  9 pfleura2 \item In the case of a VASP calculation, if input is set to Cart, then  9 pfleura2  the preamble of a VASP calculation s\item \texttt{Mopac}: Examples using sequential call  9 pfleura2  to MOPAC2009 to calculate the energies and forces along the path.  9 pfleura2 hould be added at the end of  1 pfleura2  the input file. See example file \texttt{Test\_VASP\_cart.path}.  1 pfleura2  In the case of a VASP calculation, one should also give value of the  1 pfleura2  \texttt{RunMode} variable .  9 pfleura2 \item In the case of a SIESTA calculation, an example of a Siesta input file  9 pfleura2  should be added at the end of the input file. See \texttt{Test\_Siesta.path}.  9 pfleura2 \end{itemize}  1 pfleura2 9 pfleura2 \item[RunMode:] When running on a multi-processor machine, this indicates  9 pfleura2  wether \Path{} should calculate the energy and gradient of the whole path in parallel  1 pfleura2  or not. User has two options. One is to calculate the energy and  1 pfleura2  gradient of each point sequentially. This is usefull when  1 pfleura2  running on one (or two) processors. In this case,  1 pfleura2  \texttt{RunMode} should be put to \texttt{SERIAL}.When running  1 pfleura2  in parallel with 8 or more processors, one can use VASP to  1 pfleura2  calculate simultaneously the energies and gradients for all  1 pfleura2  points, as in a normal NEB calculation. In this case,  9 pfleura2  \texttt{RunMode} must be set to \texttt{PARA}.  9 pfleura2  \emph{For now, this is usefull only for VASP.} \\  9 pfleura2 9 pfleura2 \item[ProgExe:] Name (with full path) of the executable to be used to get  1 pfleura2  energies and gradients. For example, if VASP is used in parallel, one might  1 pfleura2  have something like: \\  1 pfleura2 \verb!ProgExe='/usr/local/mpich/bin/mpirun -machinefile machine -np 8 ~/bin/VASP_46'!.  1 pfleura2 Another option that I use, is to put \verb!ProgExe='./run_vasp'! and I put every option needed to run VASP  1 pfleura2 into the \texttt{run\_vasp} file.  9 pfleura2 \item[EReac:] (REAL) By default, \Path{} does not compute the energy of the reactants  9 pfleura2  and products. This thus indicates the reactants energy to \Path{} to have better plots  9 pfleura2  at the end.  9 pfleura2 \item[EProd:] (REAL) By default, \Path{} does not compute the energy of the reactants  9 pfleura2  and products. This thus indicates the products energy to \Path{} to have better plots.  9 pfleura2 \item[PathName:] Prefix used to save the path. Default is Path  9 pfleura2 \item[Poscar:] string that will be used as the prefix for the different  1 pfleura2  POSCAR files in a VASP calculations. Usefull only if PathOnly=.TRUE.,  1 pfleura2  not used for internal calculations.  9 pfleura2 \item[CalcName:] Prefix for the files used for the energy and gradient calculations  9 pfleura2 \item[ISuffix:] Suffix for the input file used for energy and gradient calculations.  9 pfleura2 The full inputfile name will thus be \textit{CalcName}.\textit{ISuffix}.  9 pfleura2 \item[OSuffix:] Suffix for the output file used for energy and gradient calculations.  9 pfleura2  The full outputfile name will thus be \textit{CalcName}.\textit{OSuffix}.  9 pfleura2 \item[IGeomRef:] Index of the geometry used to construct the internal coordinates.  9 pfleura2  Valid only for Coord=Zmat, Hybrid or Mixed.  9 pfleura2 \item[Fact:] REAL used to define if two atoms are linked.  1 pfleura2  If $d(A,B) \leq fact*(rcov(A)+rcov(B))$, then A and B are considered Linked.  9 pfleura2 \item[debugFile:] Name of the file that indicates which subroutine should print debug info.  9 pfleura2 \item[Coord:] System of coordinates to use. Possible choices are:  9 pfleura2 \begin{itemize}  9 pfleura2 \item CART (or Xyz): works in cartesian  9 pfleura2 \item Zmat: works in internal coordinates (Zmat)  9 pfleura2 \item Mixed: frozen atoms, as well as atoms defined by the  1 pfleura2  'cart' array(see below) are describe in CARTESIAN, whereas the  1 pfleura2  others are described in Zmat  9 pfleura2 \item Baker: use of Baker coordinates, also called delocalized internal coordinates  9 pfleura2 \item Hybrid: geometries are described in zmat, but the gradient are used in cartesian  9 pfleura2 \end{itemize}  9 pfleura2 \item[Step\_method:] method to compute the step for optimizing a geometry; choices are:  9 pfleura2 \begin{itemize}  9 pfleura2 \item RFO: Rational function optimization  9 pfleura2 \item GDIIS: Geometry optimization using direct inversion in the iterative supspace  9 pfleura2 \end{itemize}  9 pfleura2 \item[HUpdate:] method to update the hessian. By default, it is Murtagh-Sargent  1 pfleura2  Except for geometry optimization where it is BFGS.  9 pfleura2 \item[MaxCyc:] maximum number of iterations for the path optimization  9 pfleura2 \item[Smax:] Maximum length of a step during path optimization  9 pfleura2 \item[SThresh:] Step Threshold to consider that the path is stationary  9 pfleura2 \item[GThresh:] Gradient Threshold to consider that the path is stationary, only orthogonal part is taken  9 pfleura2 \item[FTan:] We moving the path, this gives the proportion of the displacement tangent to the path  1 pfleura2  that is kept. FTan=1. corresponds to the full displacement,  1 pfleura2  whereas FTan=0. gives a displacement orthogonal to the path.  9 pfleura2 \item[IReparam:] The path is not reparameterised at each iteration. This gives the  9 pfleura2 frequency of reparameterization.  9 pfleura2 \item[IReparamT:] When the path is not reparameterised at each iteration, this gives the  9 pfleura2 frequency of reparameterization of the \emph{tangents}.  9 pfleura2 \item[ISpline:] By default, a linear interpolation is used to generate the path.  1 pfleura2  This option indicates the first step where spline interpolation is used.  9 pfleura2 \item[BoxTol:] Real between 0. and 1. When doing periodic calculations,  9 pfleura2  it might happen that an atom moves out of the unit cell.  9 pfleura2  Path detects this by comparing the displacement to boxtol:  9 pfleura2  if an atom moves by more than Boxtol, then it is moved back into the unit cell. Default value: 0.5.  9 pfleura2 \item[FrozTol:] (Real) This indicates the threshold to determine wether an atom moves between two images. Default is 1e-4.  9 pfleura2 \item[OptGeom:] This INTEGER indicates the index of the geometry you want to optimize.  9 pfleura2 If \texttt{OptGeom} is set, then \Path{} performs a geometry optimization instead of a path interpolation.  9 pfleura2 \item[GeomFile:] Name of the file to print the geometries and their energy  9 pfleura2  during a geometry optimization. If this variable is not given  9 pfleura2  then nothing is printed.  9 pfleura2 \item[AnaFile:] Name of the file to print the values of the geometrical parameters  9 pfleura2 that are monitored if \texttt{AnaGeom=.TRUE.}. Default is \textit{PathName}.dat  9 pfleura2 \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  9 pfleura2 %% Not described here: NMaxPtPath, NGintMax (too technical ?)  1 pfleura2 \end{description}  1 pfleura2 9 pfleura2 \subsubsection{Arrays:}  1 pfleura2 \begin{description}  9 pfleura2 \item[Rcov:] Array containing the covalent radii of the first 86 elements.  1 pfleura2  You can modify it using, \verb!rcov(6)=0.8!.  9 pfleura2 \item[Mass:] Array containing the atomic mass of the first 86 elements.  9 pfleura2 \item[AtTypes:] Name of the different atoms used in a VASP calculations.  1 pfleura2  If not given, Path will read the POTCAR file.  1 pfleura2 \end{description}  1 pfleura2 9 pfleura2 \subsubsection{Flags:}  1 pfleura2 \begin{description}  9 pfleura2 \item[MW:] Flag. True if one wants to work in Mass Weighted coordinates. Default=.TRUE.  9 pfleura2 \item[Renum:] Flag. True if one wants to reoder the atoms in the  9 pfleura2  initial order. default is .TRUE. unless for \texttt{Coord} equals \texttt{CART}.  9 pfleura2 \item[OptProd:] True if one wants to optimize the geometry of the products.  9 pfleura2 \item[OptReac:] True if one wants to optimize the geometry of the reactants.  9 pfleura2 \item[CalcEProd:] if TRUE the product energy will be  9 pfleura2  computed. Default is FALSE. Not Compatible with \texttt{RunMode=Para}.  9 pfleura2 \item[CalcEReac:] if TRUE the reactants energy will be  9 pfleura2  computed. Default is FALSE. Not Compatible with \texttt{RunMode=Para}.  9 pfleura2 \item[PathOnly:] TRUE if one wants to generate the initial path, and stops.  9 pfleura2 \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.  9 pfleura2 \item[Hinv:] if True, then Hessian inversed is used.  9 pfleura2 \item[IniHup:] if True, then Hessian inverse is extrapolated  1 pfleura2  using the initial path calculations.  9 pfleura2 \item[HupNeighbour:] if True, then Hessian inverse is  1 pfleura2  extrapolated using the neighbouring points of the path.  9 pfleura2 \item[FFrozen:] True if one wants to freeze the positions of some atoms.  1 pfleura2  If True, a \verb!&frozenlist! namelist containing the  1 pfleura2  list of frozen atoms must be given.  1 pfleura2  If VASP is used, and frozen is not given  1 pfleura2  here, the program will use the F flags of the input geometry  9 pfleura2 \item[FCart:] True if one wants to describe some atoms using cartesian coordinates.  1 pfleura2  *** Only used in 'mixed' calculations. ***  1 pfleura2  If True, a \verb!&cartlist! namelist containing the list of cart atoms must be given.  1 pfleura2  By default, only frozen atoms are described in cartesian coordinates.  1 pfleura2 9 pfleura2 \item[Autocart:] True if you want to let the program choosing the cartesian atoms.  9 pfleura2 \item[VMD:] TRUE if you want to use VMD to look at the Path. Used only for VASP for now.  9 pfleura2 \item[WriteVASP:] TRUE if you want to print the images coordinates in POSCAR files.  9 pfleura2 See also the POSCAR option. This can be used only if prog or input=VASP.  9 pfleura2 \item[AnaGeom:] If TRUE, Opt'n Path will create a file .dat for geometries analysis.  9 pfleura2  If True, Opt'n Path will look for the AnaList namelist after the Path Namelist.  9 pfleura2 \item[DynMaxStep:] if TRUE, the maximum allowed step is updated at each step, for each geometry.  9 pfleura2  If energy goes up, $Smax=Smax*0.8$, if not $Smax=Smax*1.2$.  9 pfleura2  It is ensured that the dynamical Smax is within $[0.5*SMax_0,2*Smax_0]$.  1 pfleura2 \end{description}  1 pfleura2 9 pfleura2 \subsubsection{Additional namelists:}  9 pfleura2 \begin{description}  9 pfleura2 \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: \\  9 pfleura2 \texttt{\&cartlist list = 1 2 6 12 -20 \&end} \\  9 pfleura2 will described atoms 1, 2, 6, 12, 13, 14, 15, 16, 17, 18, 19 and 20 in cartesian.  9 pfleura2 \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.  9 pfleura2 \item[\&Analist nb= \ldots{} \&end] list of variables for geometry analysis. If present and if AnaGeom=T then  9 pfleura2  Opt'n Path will read it and print the values of the variable in a .dat file  9 pfleura2  If AnaGeom is T but Analist is not given, then Path.dat just contains the energy.  9 pfleura2 Analist contains the number of variables to monitor: Nb, and is followed by the description  9 pfleura2 of the variables among:  9 pfleura2 b(ond) At1 At2  9 pfleura2 a(ngle) At1 At2 At3  9 pfleura2 d(ihedral) At1 At2 At3 At4  9 pfleura2 c NbAt At1 At2 At3 At4 At5... to create a center of mass. The centers of mass are added  9 pfleura2 at the end of the real atoms of the system.  9 pfleura2 \end{description}  9 pfleura2 9 pfleura2 \subsection{Examples}  1 pfleura2 More to come... have a look at the files provided in the  1 pfleura2 \texttt{examples} directory. In particular, you will find there three  1 pfleura2 directories containing easy-to-use examples. That is, each directory contains  1 pfleura2 all the files you need to launch the application. For now, you have working  1 pfleura2 examples for:  1 pfleura2 \begin{enumerate}  1 pfleura2 \item \texttt{Gaussian}: Examples using sequential call  1 pfleura2  to Gaussian to calculate the energies and forces along the path.  1 pfleura2 \item \texttt{VASP}: Examples using  1 pfleura2  to VASP to calculate the energies and forces along the path.  1 pfleura2 As VASP can perform NEB calculations, Path can use it in two ways:  1 pfleura2 Serial or Parallel.  1 pfleura2 \begin{itemize}  1 pfleura2 \item[Serial]  1 pfleura2 In the Serial mode, Path uses Vasp to compute the energy and forces of  1 pfleura2 each image separately (as it does for Gaussian for example).  1 pfleura2 Therefore, the INCAR file should not contain any references to the  1 pfleura2 number of images (no IMAGES command!).  1 pfleura2 1 pfleura2 \item[Parallel]  1 pfleura2 In the Parallel mode, Path uses VASP to compute at once the energies  1 pfleura2 and forces for all the images (as VASP does for a NEB calculation).  1 pfleura2 Therefore, the INCAR file MUST contain the IMAGES command.  1 pfleura2 More, the directories 00, 01, ... should exist.  1 pfleura2 1 pfleura2 \item[Home or Scratch ?]  1 pfleura2 On our local cluster, it is adviced to perform the calculations on the  1 pfleura2 /scratch directory that is local rather than on the /home that is  1 pfleura2 mounted via NFS and is thus slow.  1 pfleura2 However, when doing so, we sometimes had troubles with VASP, and  1 pfleura2 discovered that all files should be copied on the /scratch of all  1 pfleura2 machines.  1 pfleura2 Therefore, the scripts are a bit tricky.  1 pfleura2 In case your computer center is similar to ours, we provide 2 SGE  1 pfleura2 scripts:  1 pfleura2 \begin{itemize}  1 pfleura2 \item[run\_Path\_SGE\_home] performs the VASP calculations in the /home  1 pfleura2 directory  1 pfleura2 \item[run\_Path\_SGE\_scratch] creates the directories, copies the  1 pfleura2  files and performs the VASP calculations in the local /scratch  1 pfleura2  directories.  1 pfleura2 \end{itemize}  1 pfleura2 \end{itemize}  1 pfleura2 \item \texttt{Mopac}: Examples using sequential call  9 pfleura2  to MOPAC to calculate the energies and forces along the path.  9 pfleura2 \item \texttt{Siesta}: Examples using sequential call  9 pfleura2  to Siesta to calculate the energies and forces along the path.  1 pfleura2 \item \texttt{Test}: Examples using the analytical HCN potential  1 pfleura2  energy surface to calculate the energies and forces along the path.  1 pfleura2 As this is fast, we also provide other Analysis tools.  1 pfleura2 See README files in the Cart and Zmat subdirectories.  1 pfleura2 \end{enumerate}  1 pfleura2 1 pfleura2 \subsection{Path analysis}  1 pfleura2 In order to analyse the path evolution, we provide some utilities, in  1 pfleura2 the \texttt{utils} directory. \texttt{xyz2scan} and \texttt{xyz2path}  1 pfleura2 have to be compiled. For this, go to either the \texttt{src} or the  1 pfleura2 \texttt{utils} directory and type \texttt{make utils}.  1 pfleura2 Here is a brief description of these utilities.  1 pfleura2 1 pfleura2 \begin{itemize}  1 pfleura2 \item \texttt{AnaPath} and/or \texttt{AnaPathref} \\  1 pfleura2 These scripts analyse a calculated path. They use \texttt{xyz2path} to  1 pfleura2 convert the cartesian coordinates saved by \Path{} into a data file  1 pfleura2 (called PathName.datl) that be plotted using the gnuplot files that are  1 pfleura2 also created. They all plot the path energy but in different ways:  1 pfleura2 \begin{itemize}  1 pfleura2 \item[PathName\_l.gplot] plots the energy of the first iteration (the  1 pfleura2  initial path) together with the energy of the following iterations,  1 pfleura2  but one at a time.  1 pfleura2 \item[PathName\_l2.gplot] plots the energy of the path for all  1 pfleura2  iterations, with respect to the  1 pfleura2 curvilinear distance along the path.  1 pfleura2 \item[PathName\_l3.gplot] plots the energy of the path for all  1 pfleura2  iterations, with respect to the index of the images.  1 pfleura2 \end{itemize}  1 pfleura2 \item \texttt{xyz2path} and \texttt{xyz2scan} convert a bunch of  1 pfleura2  cartesian coordinates into  1 pfleura2  a data file. They are very similar: the only difference is the way  1 pfleura2  they print their results. For \texttt{xyz2scan} the analyses are  1 pfleura2  indiced using the geometry number whereas \texttt{xyz2path} computes  1 pfleura2  the mass weighted distance between two geometries and uses this  1 pfleura2  distance to index the results. \\  1 pfleura2 They both use a file called 'list' to perform the analysis, which has  1 pfleura2 the following structure: each line contains the type of the value you  1 pfleura2 want to follow, it can be:  1 pfleura2 \begin{itemize}  1 pfleura2 \item[b] for a Bond distance  1 pfleura2 \item[a] for an angle  1 pfleura2 \item[d] for a dihedral  1 pfleura2 \item[c] to create a center of mass  1 pfleura2 \end{itemize}  1 pfleura2 This descriptor is followed by the number of the atoms involved. The  1 pfleura2 exception, is the \texttt{c} command that is followed by the number of  1 pfleura2 atoms used to define this center of mass, and then the index of the atoms.  1 pfleura2 A typical file can be:  1 pfleura2 \begin{verbatim}  1 pfleura2  b 1 2  1 pfleura2  b 2 3  1 pfleura2  a 1 2 3  1 pfleura2  c 2 1 2 <- create a new atom located at the middle of the 1-2 bond.  1 pfleura2 \end{verbatim}  1 pfleura2 1 pfleura2 The cartesian geometries have to follow the XMol format. If the  1 pfleura2 comment line contains \texttt{E=} then \texttt{xyz2scan} and  1 pfleura2 \texttt{xyz2path} will read the following number and take it as the  1 pfleura2 image energy.  1 pfleura2 \end{itemize}  1 pfleura2 1 pfleura2 \end{document}