diff --git a/doc/user/constraints.tex b/doc/user/constraints.tex index 89a522ff50..86da7ce5f3 100644 --- a/doc/user/constraints.tex +++ b/doc/user/constraints.tex @@ -1,15 +1,14 @@ -\label{sec:constraints} +\label{sec:constraintsnew} The constraints directive allows the user to specify which constraints should be imposed on the system during the geometry optimization. Currently such constraints are limited to fixed atom positions and harmonic restraints (springs) on the distance between the two atoms. The -general form of constraints directive is presented below: +general form of constraints block is presented below: \begin{verbatim} CONSTRAINTS [string name ] \ [clear] \ [enable||disable] \ - [disable] \ [fix atom ] \ [spring bond ] END @@ -17,7 +16,7 @@ general form of constraints directive is presented below: \end{verbatim} The keywords are described below \begin{itemize} -\item name -- optional keyword that associates a name with a given set of +\item {\it name} -- optional keyword that associates a name with a given set of constraints. Any unnamed set of constraints will be given a name ''default'' and will be automatically loaded prior to a calculation. Any constraints with the name other than ''default'' will have to be loaded manually using @@ -37,20 +36,22 @@ SET\ directive. For example, \end{verbatim} \begin{itemize} -\item clear -- destroys any prior constraint information. This may be +\item {\it clear} -- destroys any prior constraint information. This may be useful when the same constraints have to be redefined or completely removed from the runtime database. -\item enable||disable -- enables or +\item {\it enable||disable} -- enables or disables particular set of constraints without actually removing the information from the runtime database. -\item fix atom -- fixes atom positions during geometry optimization. This +\item {\it fix atom} -- fixes atom positions during geometry optimization. This directive requires an integer list that specifies which atoms are to be -fixed. This directive can be repeated with a given constraints block. Let us -consider a case where atoms 1, 3, 4, 5, 6 need to be fixed. There are several +fixed. This directive can be repeated within a given constraints block. +To illustrate the use "{\it fix atom}" directive let us +consider a situation where we would like to fix atoms 1, 3, 4, 5, 6 while performing an optimization on some hypothetical system. +There are actually several ways to enter this particular constraint. -There is a straightforward way which requires the most typing +There is a straightforward option which requires the most typing \begin{verbatim} constraints @@ -65,7 +66,7 @@ Second method uses list input end \end{verbatim} -Third approach uses multiple fix atom directives +Third approach illustrates the use of multiple fix atom directives \begin{verbatim} constraints fix atom 1 @@ -73,15 +74,15 @@ Third approach uses multiple fix atom directives end \end{verbatim} -\item spring bond <$i j k r_0$> -- places a spring with a spring constant $k$ and equilibrium length $r_0$ -between atoms $i$ and $j$. Note that this type of constraint adds an additional term to +\item {\it spring} bond <$i j k r_0$> -- places a spring with a spring constant $k$ and equilibrium length $r_0$ +between atoms $i$ and $j$ (all in atomic units). Please note that this type of constraint adds an additional term to the total energy expression \[ E=E_{total}+\frac{1}{2}k(r_{ij}-r_0)^2 \] This additional term forces the distance between atoms $i$ and $j$ to be in the vicinity of $r_0$ but never exactly that. In general the spring energy term will always have some nonzero residual value, and this has to be accounted for when comparing total -energies. The spring bond directive can be repeated within a given constraints block. If the spring between the same pair of atoms +energies. The "{\it spring bond}" directive can be repeated within a given constraints block. If the spring between the same pair of atoms is defined more than once, it will be replaced by the latest specification in the order it appears in the input block. \end{itemize}