1% $Id$ 2\label{sec:vib} 3 4The nuclear hessian which is used to compute the vibrational 5frequencies can be computed by finite difference for any ab initio 6wave-function that has analytic gradients or by analytic methods 7for SCF and DFT (see Section \ref{sec:hess} for details). The appropriate 8nuclear hessian generation algorithm is chosen based on the user input 9when \verb+TASK <theory> frequencies+ is the task directive. 10 11The vibrational package was integrated from the Utah Messkit and can 12use any nuclear hessian generated from the driver routines, finite 13difference routines or any analytic hessian modules. There is no required 14input for the ``VIB'' package. VIB computes the Infra Red frequencies 15and intensities\footnote{Intensities are only computed if the dipole 16derivatives are available; these are computed by default for most 17methods that use the finite difference driver routines} for the 18computed nuclear hessian and the ``projected'' nuclear hessian. The 19VIB module projects out the translations and rotations of the nuclear 20hessian using the standard Eckart projection algorithm. 21It also computes the zero point energy for the molecular system 22based on the frequencies obtained from the projected hessian. 23 24The default mass of each atom is used unless an alternative mass is 25provided via the geometry input, (c.f., \ref{sec:geom}) or redefined 26using the vibrational module input. The default mass is the mass of 27the most abundant isotope of each element.\footnote{c.f., "The 28Elements" by John Emsley, Oxford University Press, (C) 1989, ISBN 290-19-855237-8.} If the abundance was roughly equal, the mass of the 30isotope with the longest half life was used. 31 32In addition, the vibrational analysis is given at the default standard 33temperature of 298.15 degrees. 34 35\section{Vibrational Module Input} 36 37All input for the Vibrational Module is optional since the default 38definitions will compute the frequencies and IR 39intensities\footnote{The geometry specification at the point where the 40hessian is computed must be the default ``geometry'' on the current 41run-time-data-base for the projection to work properly.}. The generic 42module input can begin with \verb+vib+, \verb+freq+, \verb+frequency+ 43and has the form: 44\begin{verbatim} 45 {freq || vib || frequency} 46 [reuse [<string hessian_filename>]] 47 [mass <integer lexical_index> <real new_mass>] 48 [mass <string tag_identifier> <real new_mass>] 49 [{temp || temperature} <integer number_of_temperatures> \ 50 <real temperature1 temperature2 ...>] 51 [animate [<real step_size_for_animation>]] 52 end 53\end{verbatim} 54 55\subsection{Hessian File Reuse} 56By default the \verb+task <theory> frequencies+ directive will 57recompute the hessian. To reuse the previously computed hessian you 58need only specify \verb+reuse+ in the module input block. If you 59have stored the hessian in an alternate place you may redirect the 60reuse directive to that file by specifying the path to that file. 61\begin{verbatim} 62 reuse /path_to_hessian_file 63\end{verbatim} 64This will reuse your saved Hessian data but one caveat is that the 65geometry specification at the point where the hessian is computed must 66be the default ``geometry'' on the current run-time-data-base for the 67projection to work properly. 68 69\subsection{Redefining Masses of Elements} 70You may also modify the mass of a specific center or a group of 71centers via the input. 72 73To modify the mass of a specific center you can simply use: 74\begin{verbatim} 75 mass 3 4.00260324 76\end{verbatim} 77which will set the mass of center 3 to 4.00260324 AMUs. The lexical 78index of centers is determined by the geometry object. 79 80To modify all Hydrogen atoms in a molecule you may use the tag based 81mechanism: 82\begin{verbatim} 83 mass hydrogen 2.014101779 84\end{verbatim} 85 86The mass redefinitions always start with the default masses and 87change the masses in the order given in the input. Care must be taken to change 88the masses properly. For example, if you want all hydrogens to have 89the mass of Deuterium and the third hydrogen (which is the 6th atomic 90center) to have the mass of Tritium you must set the Deuterium masses 91first with the tag based mechanism and then set the 6th center's mass 92to that of Tritium using the lexical center index mechanism. 93 94The mass redefinitions are not fully persistent on the 95run-time-data-base. Each input block that redefines masses will 96invalidate the mass definitions of the previous input block. 97For example, 98\begin{verbatim} 99freq 100 reuse 101 mass hydrogen 2.014101779 102end 103task scf frequencies 104freq 105 reuse 106 mass oxygen 17.9991603 107end 108task scf frequencies 109\end{verbatim} 110will use the new mass for all hydrogens in the first frequency 111analysis. The mass of the oxygen atoms will be redefined in the second 112frequency analysis but the hydrogen atoms will use the default mass. 113To get a modified oxygen and hydrogen analysis you would have to use: 114\begin{verbatim} 115freq 116 reuse 117 mass hydrogen 2.014101779 118end 119task scf frequencies 120freq 121 reuse 122 mass hydrogen 2.014101779 123 mass oxygen 17.9991603 124end 125task scf frequencies 126\end{verbatim} 127 128\subsection{Temp or Temperature} 129The ``VIB'' module can generate the vibrational analysis at various 130temperatures other than at standard room temperature. Either 131temp or temperature can be used to initiate this command. 132 133To modify the temperature of the computation you can simply use: 134\begin{verbatim} 135 temp 4 298.15 300.0 350.0 400.0 136\end{verbatim} 137 138At this point, the temperatures are persistant and so the user 139must "reset" the temperature if the standard behavior is required 140after setting the temperatures in a previous ``VIB'' command, i.e. 141\begin{verbatim} 142 temp 1 298.15 143\end{verbatim} 144 145\subsection{Animation} 146The ``VIB'' module also can generate mode animation input files in the 147standard xyz file format for graphics packages like 148RasMol or XMol {There are scripts to automate this for RasMol in 149{\verb+$NWCHEM_TOP/contrib/rasmolmovie+}. Each mode will have 20 xyz 150files generated that cycle from the equilibrium geometry to 5 steps in 151the positive direction of the mode vector, back to 5 steps in the 152negative direction of the mode vector, and finally back to the 153equilibrium geometry. By default these files are {\bf not} generated. 154To activate this mechanism simply use the following input directive 155\begin{verbatim} 156 animate 157\end{verbatim} 158anywhere in the frequency/vib input block. 159\subsubsection{Controlling the Step Size Along the Mode Vector} 160By default, the step size used is 0.15 a.u. which will give reliable 161animations for most systems. This can be changed via the input directive 162\begin{verbatim} 163 animate real <step_size> 164\end{verbatim} 165where \verb+<step_size>+ is the real number that is the magnitude of 166each step along the eigenvector of each nuclear hessian mode in atomic 167units. 168 169\newpage 170 171\subsection{An Example Input Deck} 172This example input deck will optimize the geometry for the given basis 173set, compute the frequencies for H$_2$O, H$_2$O at different temperatures, 174D$_2$O, HDO, and TDO. 175\begin{verbatim} 176start h2o 177title Water 178geometry units au autosym 179 O 0.00000000 0.00000000 0.00000000 180 H 0.00000000 1.93042809 -1.10715266 181 H 0.00000000 -1.93042809 -1.10715266 182end 183basis noprint 184 H library sto-3g 185 O library sto-3g 186end 187scf; thresh 1e-6; end 188driver; tight; end 189task scf optimize 190 191scf; thresh 1e-8; print none; end 192task scf freq 193 194freq 195 reuse; temp 4 298.15 300.0 350.0 400.0 196end 197task scf freq 198 199freq 200 reuse; mass H 2.014101779 201 temp 1 298.15 202end 203task scf freq 204 205freq 206 reuse; mass 2 2.014101779 207end 208task scf freq 209 210freq 211 reuse; mass 2 2.014101779 ; mass 3 3.01604927 212end 213task scf freq 214\end{verbatim} 215