more corrections and additions, pictures for Zmatrices

doc/user/ecp.tex

@@ -76,7 +76,7 @@ for a given atom or center (identified by the string \verb+tag+) denotes
 the local part of the ECP basis.  This is equivalent to the highest 
 angular momentum
 functions specified in the literature for most ECP basis sets.  The
-standard entries (\verb+s, p, d+, etc.) for \verb+shell_type+ delineate 
+standard entries ($s$, $p$, $d$, etc.) for \verb+shell_type+ delineate 
 the angular momentum projector onto the local function.  The shell type 
 label of \verb+s+ indicates the \verb+ul-s+ projector input, \verb+p+ 
 indicates the \verb+ul-p+, etc.

doc/user/geometry.tex

@@ -33,9 +33,9 @@ These are examined in the following subsections.
 \subsubsection*{{\tt NAME}}
 The default \verb+name+ for a geometry object is \verb+geometry+, and
 most modules in the code look for a geometry with this name.  The user
-can direct a module to a different geometry by assigning the string
-\verb+geomery+ to \verb+name+ using the \verb+SET+ directive (see the
-example in Section \ref{sec:set}).
+can direct a module to a geometry with a different name by assigning
+the string \verb+geomery+ to \verb+name+ using the \verb+SET+
+directive (see the example in Section \ref{sec:set}).
 
 \subsubsection*{{\tt UNITS}}
 The default units for the geometry input unit is {\AA}ngstr\"{o}m
@@ -44,7 +44,8 @@ internally.  However, the geometric coordinates can also be supplied
 in atomic units, nanometers and picometers by specifying the
 appropriate value for the \verb+UNITS+ keyword.  (Note: The default
 conversion factor used in the code to convert from {\AA}ngstr\"{o}m to
-Bohr is $1.8897265$.)
+Bohr is $1.8897265$.  A facility to change this conversion factor will
+be provided in the near future.)
 
 Possible values for the \verb+UNITS+ keyword are (only the first two
 characters need be specified)
@@ -103,7 +104,7 @@ in the body of the geometry directive are used in subsequent geometry
 optimizations.  If \verb+AUTOZ+ is specified then the user's input is
 used {\em only} to define the starting geometry and NWChem will
 automatically generate a set of internal coordinates suitable for
-geometry optimization.  See the Section \ref{sec:zcoord} for how to
+geometry optimization.  See Section \ref{sec:zcoord} for how to
 force the definition of specific internal variables in combination
 with automatically generated variables.
 
@@ -142,24 +143,25 @@ The string \verb+tag+ is the name of the atom or center and its case
 and is interpreted as follows
 \begin{itemize}
 \item If it begins with either the symbol or name of an element
-      (ignoring case) then it is thought to be an atom of that type
-      and the default charge is the atomic number adjusted for the
-      presence of ECPs (see \ref{sec:ecp}).  Additional characters can
-      be used to distinguish between atoms of the same element. E.g.,
-      the tags \verb+oxygen+, \verb+O+, \verb+o34+, \verb+olonepair+,
-      and \verb+Oxygen-ether+, will all be interpreted as being oxygen
-      atoms.  Atoms {\em must} have basis functions associated with
-      them (Section \ref{sec:basis}). 
-    \item If the tag begins with either \verb+BQ+ or \verb+X+
-      (ignoring case) then it is treated as a dummy center with
-      default zero charge. Dummy centers may optionally have basis
-      functions or non-zero charge.  Note, that in order to recogonize
-      the xenon atom (Xe) it is not possible to input a dummy atom 
-      beginning with the characters \verb+XE+ --- an attempt to do
-      this will generate a xenon atom.
-    \item {\em If the tag begins with characters that cannot be
-        matched against an atom or \verb+BQ+ or \verb+X+ then a fatal
-        error is generated.}
+  (ignoring case) then it is thought to be an atom of that type
+  and the default charge is the atomic number adjusted for the
+  presence of ECPs (see \ref{sec:ecp}).  Additional characters can
+  be used to distinguish between atoms of the same element. E.g.,
+  the tags \verb+oxygen+, \verb+O+, \verb+o34+, \verb+olonepair+,
+  and \verb+Oxygen-ether+, will all be interpreted as being oxygen
+  atoms.  Atoms {\em must} have basis functions associated with
+  them (Section \ref{sec:basis}). 
+\item If the tag begins with either \verb+BQ+ or \verb+X+
+  (ignoring case) then it is treated as a dummy center with
+  default zero charge. Dummy centers may optionally have basis
+  functions or non-zero charge.  Note, that in order to recogonize
+  the xenon atom (Xe) it is not possible to input a dummy atom 
+  beginning with the characters \verb+XE+ --- an attempt to do
+  this will generate a xenon atom.  See Section \ref{sec:sample2} for
+  a sample input using dummy centers with charges.
+\item {\em If the tag begins with characters that cannot be
+    matched against an atom or \verb+BQ+ or \verb+X+ then a fatal
+    error is generated.}
 \end{itemize}
 
 It is {\em important} to be aware of the following points
@@ -176,9 +178,9 @@ and any net total charge of the system (Section \ref{sec:charge}) are
 used to determine the number of electrons.
 \end{itemize}
 
-The Cartesian coordinates of the atom in the molecule are specified as real
-numbers following the string \verb+tag+.  The user also has the option
-of specifying the charge of the atom (or center) and its mass.
+The Cartesian coordinates of the atom in the molecule are specified as
+real numbers following the tag.  The user also has the option of
+specifying the charge of the atom (or center) and its mass.
 
 The default charge for an atom is its atomic number, adjusted for the
 presence of ECPs (see Section \ref{sec:ecp}).  In order to specify a
@@ -213,12 +215,12 @@ coordinates (bond lengths, bond angles and dihedral angles).  The
 Z-matrix input for a center consists of pairs numbers that define
 connectivity indices and a bond length and bond or torsion angless.
 Cartesian coordinate input consists of three real numbers defining the
-x,y,z coordinates of the atom.  {\em Within the Z-matrix input bond
-  lengths and cartesian coordinates must presently be specified in
-  {\AA}ngstr{\"o}ms, regardless of the entry specified for
-  \verb+units+.} Angles are specified in degrees.
+x,y,z coordinates of the atom.  
+
+Within the Z-matrix input bond lengths and cartesian coordinates must
+be input in the used specified units.  Angles are specified in
+degrees.
 
-%
 % When  two  numerical  values,  separated by a comma, are given for some
 % variables, they are considered as the initial and final values for the
 % definition of a Linearized Synchronous Transit pathway.  The
@@ -236,7 +238,8 @@ Bond lengths, bond angles and dihedral angles (denoted below as {\tt
   R}, {\tt alpha}, {\tt beta} respectively) may be specified either as
 numerical values or as symbolic strings which are subsequently
 defined.  The same sybmolic string may be used several times.  Any
-mixture of numeric data and symbols may be given. 
+mixture of numeric data and symbols may be given. Bond angles
+($\alpha$) must be in the range $0 < \alpha < 180$.
 
 The Z-matrix input is specified sequentially as follows
 \begin{verbatim}
@@ -249,13 +252,15 @@ The Z-matrix input is specified sequentially as follows
 
 We examine this in more detail.  In the following, the tag or number
 of the center being currently defined is labelled as \verb+C+ (``C''
-for current).  Figures \ref{fig:zmat1}, \ref{fig:zmat2} and
-\ref{fig:zmat3} display the relationship between the input data 
-and the definition of centers and angles.
+for current).  The above discussion on the interpretation of tags
+(Section \ref{sec:cart}) also applies to centers defined in Z-matrix
+input.  Figures \ref{fig:zmat1}, \ref{fig:zmat2} and \ref{fig:zmat3}
+display the relationship between the input data and the definition of
+centers and angles.
 
 \begin{figure}[htbp]
 \centering
-\psfig{figure=zmat1.eps}
+\psfig{figure=zmat1.eps,angle=270,width=6in}
 
 \caption{\label{fig:zmat1} Relationship between the centers, bond angle
 and dihedral angle in Z-matrix input.}
@@ -263,7 +268,7 @@ and dihedral angle in Z-matrix input.}
 
 \begin{figure}[htbp]
 \centering
-\psfig{figure=zmat2.eps}
+\psfig{figure=zmat2.eps,angle=270,width=6in}
 
 \caption{\label{fig:zmat2} Relationship between the centers and two
   bond angles in Z-matrix input with optional parameter specified as $+1$.}
@@ -271,7 +276,7 @@ and dihedral angle in Z-matrix input.}
 
 \begin{figure}[htbp]
 \centering
-\psfig{figure=zmat3.eps}
+\psfig{figure=zmat3.eps,angle=270,width=6in}
 
 \caption{\label{fig:zmat3} Relationship between the centers and two
   bond angles in Z-matrix input with optional parameter specified as $-1$.}
@@ -459,3 +464,46 @@ specified using number of the centers.
   \verb+l+ must not be colinear.  The two bends are constructed to be
   within and perpendicular to the plane containing the atoms.
 \end{itemize}   
+
+\subsection{Freezing atoms in geometry optimizations}
+\label{sec:activeatoms}
+
+Currently the only mechanism for freezing coordinates during a
+geometry optimization is to freeze the Cartesian coordinates of a list
+of centers.  This is useful for such purposes as optimizing a molecule
+absorbed on the surface of a cluster with fixed geometry.  Only the
+gradients associated with the active atoms are computed and this can
+result in a big computational saving.  Gradients associated with
+frozen atoms are forced to zero (note that this destroys certain
+translational and rotational invariance properties).
+
+The \verb+SET+ directive (Section \ref{sec:set}) must be used as
+follows
+\begin{verbatim}
+  set geometry:actlist <integer list_of_center_number>
+\end{verbatim}
+This defines the centers in the list as being active --- all other
+centers will have zero force assigned to them and will remain frozen
+at their starting coordinates during a geometry optimization.
+
+For instance, the following directive specifies that atom numbers 1,
+5, 6, 7, 8, and 15 are active and all other atoms are frozen:
+\begin{verbatim}
+  set geometry:actlist 1 5:8 15
+\end{verbatim}
+or equivalently
+\begin{verbatim}
+  set geometry:actlist 1 5 6 7 8 15
+\end{verbatim}
+
+
+To revert to the default behaviour of all atoms active we
+must explicitly delete this entry from the database (since
+the database is persistent Section \ref{sec:persist}) as follows
+\begin{verbatim}
+  unset geometry:actlist
+\end{verbatim}
+
+
+
+

doc/user/intro.tex

@@ -535,9 +535,9 @@ to be eliminated)
 \item \verb+...+ is used to indicate indefinite continuation of a list
 \end{itemize}
 
-An input parameter is identified in the description of the
-directive by prefacing the item with the name of the type of data expected;
-i.e., 
+An input parameter is identified in the description of the directive
+by prefacing the item with the name of the type of data expected;
+i.e.,
 
 \begin{itemize}
 \item \verb+string +  -- an ASCII character string
@@ -751,6 +751,7 @@ tasks is expected to change in the future, but the directive for
 specifying names should remain the same.)
 
 \subsection{Persistence of data and restart}
+\section{sec:persist}
 
 The database is persistent, meaning that all input data and results
 that are not destroyed in the course of execution are permanently

doc/user/sample.tex

@@ -1,5 +1,6 @@
 \label{sec:sample}
 \subsection{Water SCF calculation and geometry optimization in a 6-31g basis}
+\label{sec:sample1}
 
 The input file in section \ref{sec:getstart} performs a geometry optimization
 in a single task.  Here we perform a single point SCF energy calculation and then
@@ -40,6 +41,7 @@ final energy and geometry should be $-75.9853591759$, O
 $(0,0,0.1563305320)$, and H $(0, \pm1.48372809, -0.853122128)$.
 
 \subsection{Compute the polarizability of Ne using finite field}
+\label{sec:sample2}
 
 \subsubsection{Job 1. Compute the atomic energy}
 
@@ -82,6 +84,7 @@ the interaction between the two point charges in the total energy
 (section \ref{sec:geom}).
 
 \subsection{Compute the SCF energy of H$_2$CO using ECPs for C and O}
+\label{sec:sample3}
 
 The following will compute the SCF energy for formaldehyde with ECPs
 on the Carbon and Oxygen centers.

doc/user/scfgrad.tex

@@ -1,15 +1,4 @@
-\subsection{Hartree-Fock or SCF Gradients}
-
-\Large
-***This should be part of the SCF section (Section 8, in the current
-numbering; it doesn't belong all on its own as a separate Section 9),
- since
-it appears to be part of the SCF module input.****
-\normalsize
-
-The input for this directive allows the user to define some important
-characteristics of the Hartree-Fock gradients for the SCF, UHF and ROHF
-calculations.  The form of the directive is as follows;
+\label{sec:scfgrad}
 
 \begin{verbatim}
   GRADIENTS 
@@ -21,6 +10,12 @@ calculations.  The form of the directive is as follows;
 
 %  This input controls the Hartree-Fock (SCF, UHF and ROHF) gradients.  
 
+The input for this directive allows the user to define 
+characteristics of the Hartree-Fock gradients for the SCF, UHF and ROHF
+calculations.  The form of the directive is as follows;
+
+
+
 The directive contains two keywords, \verb+chkpt+ and \verb+restart+,
 that are related to the creation of the gradients.  The keyword \verb+chkpt+
 allows the user to specify a time interval at which the current values
@@ -79,26 +74,4 @@ via print control.  These are as follows;
         'timing'   \>             default \> 
 \end{tabbing}
 
-\subsection{frozen atoms}
-\label{sec:activeatoms}
-
-\Large
-***This section belongs somewhere near where you explain about atoms
-and centers and frozen atoms; somewhere in the section on Geometry,
-or maybe Basis sets, I suspect.  It definitely does not belong here,
-all on its lonesome.***
-\normalsize
-
-Currently the only mechanism for freezing atoms is to enter a list of
-active atoms via the \verb+SET+ directive.
-
-\begin{verbatim}
-  set geometry:actlist integer <at1> <at2> <at3> ...
-\end{verbatim}
-defines atoms number \verb+<at1>+ \ldots as 'active', and only forces
-on those are calculated. All other atoms remain frozen at their
-starting coordinates during a geometry optimization.
-% I have no idea how this works with symmetry.
-% But in the new release there will be frozen atoms and variables
-% anyway.
 

doc/user/user.tex

@@ -44,7 +44,7 @@
 \section{Hartree-Fock or Self-consistent Field: SCF Module} 
 \input{scf}
 
-% \section{Hartree-Fock or SCF gradients}
+\section{Hartree-Fock or SCF Gradients}
 \input{scfgrad}
 
 \section{Gaussian Density Functional Theory (DFT) Module}