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Consistency for section headings, references, formatting fixes

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Robert Harrison 1997-02-21 16:48:22 +00:00
parent aaa40332e2
commit 4e3e2b05da
12 changed files with 80 additions and 88 deletions
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2
doc/user/basis.tex
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@ -89,7 +89,7 @@ the same \verb+tag+ will have the same basis set. All atoms must have
basis functions assigned to them --- only dummy centers may have no
basis functions.
We examine next how to reference standard basis sets in the basis set
Examined next is how to reference standard basis sets in the basis set
library, and, finally, how to define a basis using exponents and
coefficients.

8
doc/user/ccsd.tex
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@ -27,7 +27,7 @@ regardless of the actual level of theory desired (specified with the
\verb+TASK+ directive). The following directives are recognized
within the \verb+CCSD+ group.
\subsubsection{MAXITER}
\subsubsection{{\tt MAXITER} --- Maximum number of iterations}
The maximum number of iterations is set to 20 by default. This should
be quite enough for most calculations, although particularly
@ -37,7 +37,7 @@ troublesome cases may require an increase.
MAXITER <integer maxiter default 20>
\end{verbatim}
\subsubsection{THRESH}
\subsubsection{{\tt THRESH} --- Convergence threshold}
Controls the convergence threshold for the iterative part of the
calculation. Both the RMS error in the amplitudes {\em and} the
@ -47,7 +47,7 @@ change in energy must be less than $10^{-{\tt thresh}}$.
THRESH <integer thresh default 6>
\end{verbatim}
\subsubsection{DIISBAS}
\subsubsection{{\tt DIISBAS} --- DIIS subspace dimension}
Specifies the maximum size of the subspace used in DIIS convergence
acceleration. Note that DIIS requires the amplitudes and errors be
@ -63,7 +63,7 @@ storage are being considered, but have not yet been implemented.}
DIISBAS <integer diisbas default 5>
\end{verbatim}
\subsubsection{IPRT}
\subsubsection{{\tt IPRT} --- Debug printing}
This directive controls the level of output from the code, mostly to
facilitate debugging and the like. The larger the value, the more

17
doc/user/dplot.tex
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@ -11,7 +11,7 @@ on a specified set of grid points using the molecular orbitals
from SCF or DFT calculation. An input file to the {\em Insight}
program is then generated. Different sub-directives are described below.
\subsection{Title}
\subsection{{\tt TITLE} --- Title for {\em Insight}}
\begin{verbatim}
TITLE
@ -21,9 +21,7 @@ program is then generated. Different sub-directives are described below.
This sub-directive specifies a title line for the generated
input to the {\em Insight} program. Only one line is allowed.
\subsection{LimitXYZ}
\subsection{{\tt LIMITXYZ} --- Plot limits}
\begin{verbatim}
LIMITXYZ [units <string Units default angstrom>]
@ -39,7 +37,7 @@ along each direction. The known names for \verb+Units+ are
\subsection{Spin}
\subsection{{\tt SPIN} --- Density to be plotted}
\begin{verbatim}
SPIN <string Spin default total>
@ -52,7 +50,7 @@ $\alpha$ and $\beta$ electron densities.
\subsection{Output}
\subsection{{\tt OUTPUT} --- Filename for {\em Insight}}
\begin{verbatim}
OUTPUT <string File_Name default dplot>
@ -64,7 +62,7 @@ standard NWCHEM output (LuOut).
\subsection{Vectors}
\subsection{{\tt VECTORS} --- MO vector file name}
\begin{verbatim}
VECTORS <string File_Name default movecs> [<string File_Name2>]
@ -77,7 +75,7 @@ files have to match.
\subsection{Where}
\subsection{{\tt WHERE} --- Density evaluation}
\begin{verbatim}
WHERE <string Where default grid>
@ -92,8 +90,7 @@ the position of the nuclei and written to the NWChem output) and
\verb+g++\verb+n+ (both).
\subsection{Orbitals}
\subsection{{\tt ORBITAL} --- Orbital sub-space}
\begin{verbatim}
ORBITALS [<string Option default density>]

5
doc/user/functionality.tex
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@ -28,13 +28,12 @@ second derivatives are computed by finite difference of the energy.
For all methods, the following operations may be performed
\begin{itemize}
\item Single point energy.
\item Geometry Optimization (Minimization and Transition State).
\item Numerical first and second derivatives automatically computed if
analytic derivatives are not available.
\item Geometry Optimization (Minimization and Transition State).
\item Generation of the electron density file for the {\em Insight}
graphical program.
\item Interface to
\item
\end{itemize}
In addition, automatic interfaces are provided to

41
doc/user/geometry.tex
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@ -10,8 +10,9 @@ long and complicated when presented in its general form, as follows,
\begin{verbatim}
GEOMETRY [<string name default geometry>] \
[units <string units default angstrom>] \
[bqbq] \
[print [xyz] || noprint] \
[center || nocenter] \
[bqbq] \
[autoz]
[SYMMETRY [GROUP] <string group_name> [print]]
@ -20,7 +21,7 @@ long and complicated when presented in its general form, as follows,
... ]
[ZMATRIX || ZMT || ZMAT
<string tagn> <list_of_zmatrix_variables> [ghost]
<string tagn> <list_of_zmatrix_variables>
... ]
[VARIABLES
@ -119,6 +120,12 @@ the output associated with the geometry. In addition, the keyword
be qualifed by the additional keyword \verb+xyz+, which specifies
that the coordinates should be printed in the XYZ format of XMol.
\item \verb+center+ and \verb+nocenter+ -- complimentary keyword pair
to enable or disable translation of the center of nuclear charge of
the users input molecular coordinates to the origin. With the
origin at this position all three components of the nuclear dipole
are zero. The default is to move the origin.
% \subsubsection*{{\tt AUTOZ}}
\item \verb+autoz+ -- keyword to specify that the geometry
information supplied
@ -273,20 +280,20 @@ The values supplied for the coordinates must be in the units specified
by the value of the variable \verb+<units>+ on the first line of
the \verb+GEOMETRY+ directive input.
The cartesian coordinate input line also contains
the optional keywords \verb+charge+ and \verb+mass+, which allow
the user to specify 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
different value for the charge on a particular atom, the user must
enter the keyword \verb+charge+, followed by the desired charge entered
for the variable \verb+<charge>+.
The cartesian coordinate input line also contains the optional
keywords \verb+charge+ and \verb+mass+, which allow the user to
specify the charge of the atom (or center) and its mass (in atomic
mass units). 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 different value for the charge on a particular
atom, the user must enter the keyword \verb+charge+, followed by the
desired charge entered for the variable \verb+<charge>+.
The default mass for an atom is taken to be the mass of its most abundant
naturally occurring isotope. If the user wishes to model some other
isotope of the element, its mass must be defined explicitly by
specifying the keyword \verb+mass+, followed by the mass of the isotope
entered for the variable \verb+<mass>+.
The default mass for an atom is taken to be the mass of its most
abundant naturally occurring isotope. If the user wishes to model
some other isotope of the element, its mass must be defined explicitly
by specifying the keyword \verb+mass+, followed by the mass (in atomic
mass units) of the isotope entered for the variable \verb+<mass>+.
The geometry of the system can be entirely specified by Cartesian coordinates,
by supplying a \verb+<tag>+ line of the type described above. The user has
@ -309,7 +316,7 @@ compound \verb+ZMATRIX+
directive is as follows;
\begin{verbatim}
[ZMATRIX || ZMT || ZMAT
<string tagn> <list_of_zmatrix_variables> [ghost]
<string tagn> <list_of_zmatrix_variables>
... ]
[VARIABLES
@ -552,7 +559,7 @@ internal coordinates. These are arranged as follows:
\item The third center is placed in the z-x plane.
\end{itemize}
\subsection{{\tt ZCOORD} --- Defining internal coordinates for {\tt AUTOZ}}
\subsection{{\tt ZCOORD} --- Forcing internal coordinates}
\label{sec:zcoord}
Specifying the keyword \verb+AUTOZ+ on the first line of the \verb+GEOMETRY+

26
doc/user/intro.tex
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@ -523,12 +523,11 @@ Dunning DZ+ must appear in a directive as \verb+"modified Dunning
DZ"+, since the name consists of three separate words.
A (physical) line in the input file is terminated with a newline
character (also known as a 'return' or 'enter' character). A semicolon
(\verb+;+)
can be also used to indicate the
end of an input line, allowing a given physical line of input to contain
multiple logical lines of input. For example, five lines of input for
the \verb+GEOMETRY+ directive can be entered as follows;
character (also known as a 'return' or 'enter' character). A
semicolon (\verb+;+) can be also used to indicate the end of an input
line, allowing a given physical line of input to contain multiple
logical lines of input. For example, five lines of input for the
\verb+GEOMETRY+ directive can be entered as follows;
\begin{verbatim}
geometry
O 0 0 0
@ -548,14 +547,12 @@ or until an \verb+EOF+ directive is encountered\footnote{The
(ignoring case) on a line by itself. This is a convenience that
allows unused input to be left in the same file.}.
Directives consist of a directive name, keywords, and optional input,
and may contain of one line or many. Simple directives consist of a
single line of input with one or more fields. Compound directives can
have multiple input lines, and can also include other optional
simple and compound directives. A compound directive is terminated with
an END
directive. The directives START (see Section \ref{sec:start}) and
have multiple input lines, and can also include other optional simple
and compound directives. A compound directive is terminated with an
END directive. The directives START (see Section \ref{sec:start}) and
ECHO (see Section \ref{sec:echo}) are examples of simple directives.
The directive GEOMETRY (see Section \ref{sec:geom}) is an example of a
compound directive.
@ -571,12 +568,15 @@ descriptions of the NWChem input in the following sections.
\begin{itemize}
\item a directive name always appears in all-capitals, in computer-type
face; (e.g.; \verb+GEOMETRY+, \verb+BASIS+, \verb+SCF+)
face; (e.g.; \verb+GEOMETRY+, \verb+BASIS+, \verb+SCF+). Note that
the case of directives is ignored in the actual input.
\item a keyword always appears in lower case, in computer-type face; (e.g.,
{\tt swap}, {\tt print}, {\tt units}, {\tt bqbq})
\item variable names always appear in lower case, in computer-type face,
and enclosed in angle brackets to distinguish them from keywords (e.g.,
{\tt <input\_filename>}, {\tt <basisname>}, {\tt <tag>})
\item \verb+$variable$+ is used to indicate the substitution of the value of a
variable
\item a string, token, or field is a sequence of ASCII characters (NOTE: if
the string includes blanks or tabs (i.e., white space) the entire string must
be enclosed in quotes)
@ -595,8 +595,6 @@ line within a physical line of input
\item \verb+#+ (the hash or pound symbol) is the comment character. All
characters following \verb+#+ (up to the physical end of the line) are ignored.
\item \verb+$variable$+ is used to indicate the substitution of the value of a
variable
\item \verb+...+ is used to indicate indefinite continuation of a list
\end{itemize}

1
doc/user/mp2.tex
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@ -1,4 +1,5 @@
\label{sec:mp2}
\label{sec:rimp2}
\Large
***need a brief summary here of what the MP2 modules do. Will the input
module be finished in time for the release of the code in March (or is

5
doc/user/sample.tex
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@ -3,8 +3,9 @@
\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
restart it to perform the optimization.
in a single task. A single point SCF energy calculation is performed and then
restarted to perform the optimization (both could of course be
performed in a single task).
\subsubsection{Job 1. Single point SCF energy}

4
doc/user/scf.tex
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@ -125,6 +125,7 @@ calculation. It is thus advisable when specifying \verb+ADAPT OFF+ to
also specify \verb+SYM OFF+ (Section \ref{sec:sym}).
\subsection{{\tt TOL2E} --- integral screening threshold}
\label{sec:tol2e}
\begin{verbatim}
TOL2E <real tol2e default 0.01*$thresh$>
@ -391,6 +392,7 @@ The following sets the maximum no. of SCF iterations to 50
\end{verbatim}
\subsection{{\tt RI} --- resolution of the identity approximation}
\label{sec:riscf}
The resolution of the identity (RI) approximation (using the
V-approximation of Alml\"{o}f and Vahtras) is automatically invoked if
@ -669,7 +671,7 @@ reliably with the default options for a wide variety of molecules. In
addition it should be guaranteed to converge sufficient iterations for
any system. Please report significant convergence problems to
\verb+nwchem+-\verb+support@+\-\verb+emsl.pnl.gov+, including the
input file. If we do not know about problems we cannot fix them.
input file.
% An understanding of the output of the SCF program and the options
% controlling convergence requires some knowledge of the convergence

2
doc/user/selci.tex
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@ -42,7 +42,7 @@ A typical sequence of calculations is as follows:
previous} selection threshold.
\end{enumerate}
To illustrate this we provide some abreviated output from a
To illustrate this, below is some abreviated output from a
calculation on water in an augmented cc-PVDZ basis set with one frozen
core orbital. The SCF was converged to high precision in $C_{2v}$
symmetry with the following input

53
doc/user/top-level.tex
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@ -16,7 +16,7 @@ are ignored.
The following subsections describe each of the start-up directives in detail,
noting all keywords, options, required input, and defaults.
\subsection{{\tt START}, {\tt CONTINUE} and {\tt RESTART} Directives}
\subsection{{\tt START}, {\tt CONTINUE} and {\tt RESTART} --- Startup mode}
\label{sec:start}
A {\tt START}, or {\tt CONTINUE}, or {\tt RESTART} directive is
@ -37,11 +37,15 @@ following format;
The \verb+START+ directive indicates that the calculation is one in
which the database is to be created. Any relevent information that
already exists in a previous database of the same name is destroyed.
The string variable{\tt <file\_prefix>} will be used as the prefix when naming
any files created in the course of the calculation. If the user does
not specify an entry for {\tt <file\_prefix>} on the \verb+START+
directive (or omits the \verb+START+ directive altogether), the code
assigns the the file prefix of the input file itself to {\tt <file\_prefix>}.
The string variable{\tt <file\_prefix>} will be used as the prefix
when naming any files created in the course of the calculation. If
the user does not specify an entry for {\tt <file\_prefix>} on the
\verb+START+ directive (or omits the \verb+START+ directive
altogether), the code uses the basename of the input file as the file
prefix (i.e., the name of the input file with any directory
information and the last ``dot-prefix'' removed. E.g., the input file
name \verb+/home/dave/job.2.in+ yields \verb+job.2+ as the file
prefix.).
The user also has the option of
specifying a unique name for the database, using the keyword {\tt
@ -125,7 +129,7 @@ the code behaves as if the input file contained the directive,
\end{verbatim}
\subsection{{\tt SCRATCH\_DIR} and {\tt PERMANENT\_DIR} Directives}
\subsection{{\tt SCRATCH\_DIR} and {\tt PERMANENT\_DIR} --- File directories}
\label{sec:dirs}
% This is a startup directive (section \ref{sec:inputstructure}).
@ -150,23 +154,6 @@ systems, while on the KSR it is useful to specify scratch file directories
with automated striping across processors with round-robin allocation.
SMP clusters have both requirements.
The anticipated usage of the
EMSL IBM SP has NWChem executing in \verb+scratch+ with all files
being created there by default. Files to be saved for restart {\em
must} be either explicitly redirected or copied. This has the
advantages of minimizing very expensive network traffic on shared-file
systems and also reduces the amount of data stored in the limited
shared-file space. However, this manual copying fails if the job
crashes or runs out of time, so it may be preferable to automatically
store {\em small} restart files directly to a persistent file space.
\Large
**Do we need to tell them 'anticipated' usage for the EMSL machine? It
could serve as another example, or we could delete this paragraph
entirely. Or we could put in the
'actual' usage, once it is known.***
\normalsize
The \verb+SCRATCH_DIR+ and \verb+PERMANENT_DIR+ directives have
identical format and capability, and enable the user to specify a
single directory for all processes, or different directories for
@ -227,7 +214,7 @@ given list of directories;
\end{verbatim}
\end{itemize}
\subsection{{\tt MEMORY} Directive}
\subsection{{\tt MEMORY} --- Control of memory limits}
This is a start-up directive that allows the user to specify the
amount of memory that NWChem can use for the job. If this directive
@ -365,7 +352,7 @@ Sun & 48 \\
\end{tabular}
\end{table}
\subsection{{\tt ECHO} Directive}
\subsection{{\tt ECHO} --- Print input file}
\label{sec:echo}
This start-up directive is provided as a convenient means to include a
@ -380,7 +367,7 @@ keywords, arguments, or options, and consists of the single line,
The \verb+ECHO+ directive is processed only
once, by Process 0 when the input file is read.
\subsection{{\tt TITLE} Directive}
\subsection{{\tt TITLE} --- Specify job title}
This top-level directive allows the user to identify a job or series of
jobs that use a
@ -411,7 +398,7 @@ Alternatively, since a semicolon can be used to denote the end an input line
The title is stored in the database and will be used in all subsequent
tasks/jobs until redefined in the input.
\subsection{{\tt PRINT} and {\tt NOPRINT} Directives}
\subsection{{\tt PRINT} and {\tt NOPRINT} --- Print control}
\label{sec:printcontrol}
The \verb+PRINT+ and \verb+NOPRINT+ directives allow the user to
@ -497,7 +484,7 @@ of its calling layer. (Users should send their preferences for these
defaults via email to \verb+nwchem-support@emsl+, for consideration in
future releases of the code.)
\subsection{{\tt SET} Directive}
\subsection{{\tt SET} --- Enter data in the RTDB}
\label{sec:set}
This top-level directive allows the user to enter data directly into the
@ -568,7 +555,7 @@ Additional examples of applications of this
directive can be found in the sample input files (see Section
\ref{sec:realsample}), including examples of its usage with basis sets.
\subsection{{\tt UNSET} Directive}
\subsection{{\tt UNSET} --- Delete data in the RTDB}
\label{sec:unset}
This directive gives the user a way to delete simple entries from the
@ -602,7 +589,7 @@ deleting all database entries beginning with \verb+scf:+, using the directive,
unset scf:*
\end{verbatim}
\subsection{{\tt STOP} Directive}
\subsection{{\tt STOP} --- Terminate processing}
This top-level directive provides a convenient way of verifying
an input file without actually running the calculation. It consists
@ -615,7 +602,7 @@ of the single line,
As soon as this directive is encountered, all processing ceases and
the calculation terminates with an error condition.
\subsection{{\tt TASK} Directive}
\subsection{{\tt TASK} --- Perform a task}
\label{sec:task}
The \verb+TASK+ directive is used to tell the code what to do with the
@ -811,7 +798,7 @@ executing all but the simplest commands, it is usually much easier to
put the shell script in a file and execute the file from within
NWChem.
\subsection{{\tt CHARGE} Directive}
\subsection{{\tt CHARGE} --- Total system charge}
\label{sec:charge}
This is an optional top-level directive that allows the user to specify

4
doc/user/vib.tex
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@ -6,7 +6,7 @@ driver routines.
{\it The input module for vib is under development and incomplete.}
\subsection{VIB input: project}
\subsection{Project out translations and rotations}
The VIB module can project out the translations and rotations of the
hessian using the standard Eckart projection algorithm. To set this
@ -16,7 +16,7 @@ option you must enter the following in your input deck.
set "vib:project" true
\end{verbatim}
\subsection{VIB input: zero point energy}
\subsection{Zero point energy}
The VIB module can also compute the zero point energy for the
molecular system. This will automatically set the projection flag to