From 4e3e2b05da340166bead27192aec8a7be223ee9b Mon Sep 17 00:00:00 2001 From: Robert Harrison Date: Fri, 21 Feb 1997 16:48:22 +0000 Subject: [PATCH] Consistency for section headings, references, formatting fixes --- doc/user/basis.tex | 2 +- doc/user/ccsd.tex | 8 +++--- doc/user/dplot.tex | 17 +++++------- doc/user/functionality.tex | 5 ++-- doc/user/geometry.tex | 41 +++++++++++++++++------------ doc/user/intro.tex | 26 +++++++++---------- doc/user/mp2.tex | 1 + doc/user/sample.tex | 5 ++-- doc/user/scf.tex | 4 ++- doc/user/selci.tex | 2 +- doc/user/top-level.tex | 53 ++++++++++++++------------------------ doc/user/vib.tex | 4 +-- 12 files changed, 80 insertions(+), 88 deletions(-) diff --git a/doc/user/basis.tex b/doc/user/basis.tex index e680127fa0..dea203e5e9 100644 --- a/doc/user/basis.tex +++ b/doc/user/basis.tex @@ -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. diff --git a/doc/user/ccsd.tex b/doc/user/ccsd.tex index 6df08b0dc4..cc21c0a8da 100644 --- a/doc/user/ccsd.tex +++ b/doc/user/ccsd.tex @@ -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 \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 \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 \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 diff --git a/doc/user/dplot.tex b/doc/user/dplot.tex index 6b0280ce73..f14136c7ce 100644 --- a/doc/user/dplot.tex +++ b/doc/user/dplot.tex @@ -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 ] @@ -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 @@ -52,7 +50,7 @@ $\alpha$ and $\beta$ electron densities. -\subsection{Output} +\subsection{{\tt OUTPUT} --- Filename for {\em Insight}} \begin{verbatim} OUTPUT @@ -64,7 +62,7 @@ standard NWCHEM output (LuOut). -\subsection{Vectors} +\subsection{{\tt VECTORS} --- MO vector file name} \begin{verbatim} VECTORS [] @@ -77,7 +75,7 @@ files have to match. -\subsection{Where} +\subsection{{\tt WHERE} --- Density evaluation} \begin{verbatim} WHERE @@ -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 [] diff --git a/doc/user/functionality.tex b/doc/user/functionality.tex index 8d0d89121e..cd4c6cb1a8 100644 --- a/doc/user/functionality.tex +++ b/doc/user/functionality.tex @@ -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 diff --git a/doc/user/geometry.tex b/doc/user/geometry.tex index 07a6827fd3..d91a4afa8f 100644 --- a/doc/user/geometry.tex +++ b/doc/user/geometry.tex @@ -10,8 +10,9 @@ long and complicated when presented in its general form, as follows, \begin{verbatim} GEOMETRY [] \ [units ] \ - [bqbq] \ [print [xyz] || noprint] \ + [center || nocenter] \ + [bqbq] \ [autoz] [SYMMETRY [GROUP] [print]] @@ -20,7 +21,7 @@ long and complicated when presented in its general form, as follows, ... ] [ZMATRIX || ZMT || ZMAT - [ghost] + ... ] [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++ 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++. +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++. -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++. +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++. The geometry of the system can be entirely specified by Cartesian coordinates, by supplying a \verb++ 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 - [ghost] + ... ] [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+ diff --git a/doc/user/intro.tex b/doc/user/intro.tex index f948e48810..dae1e0155d 100644 --- a/doc/user/intro.tex +++ b/doc/user/intro.tex @@ -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 }, {\tt }, {\tt }) +\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} diff --git a/doc/user/mp2.tex b/doc/user/mp2.tex index 0b2118234c..e9d198a05e 100644 --- a/doc/user/mp2.tex +++ b/doc/user/mp2.tex @@ -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 diff --git a/doc/user/sample.tex b/doc/user/sample.tex index c3f882ba18..611445a853 100644 --- a/doc/user/sample.tex +++ b/doc/user/sample.tex @@ -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} diff --git a/doc/user/scf.tex b/doc/user/scf.tex index e1c9d3e5dd..13cd79bf5f 100644 --- a/doc/user/scf.tex +++ b/doc/user/scf.tex @@ -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 @@ -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 diff --git a/doc/user/selci.tex b/doc/user/selci.tex index 046cdf74ca..88f442fba0 100644 --- a/doc/user/selci.tex +++ b/doc/user/selci.tex @@ -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 diff --git a/doc/user/top-level.tex b/doc/user/top-level.tex index 0f0cf20125..d1f765cea7 100644 --- a/doc/user/top-level.tex +++ b/doc/user/top-level.tex @@ -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 } 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 } 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 }. +The string variable{\tt } 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 } 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 diff --git a/doc/user/vib.tex b/doc/user/vib.tex index 69fa43e4ed..5e2400a52f 100644 --- a/doc/user/vib.tex +++ b/doc/user/vib.tex @@ -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