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6
doc/prog/GNUmakefile
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@ -25,7 +25,11 @@
TARG = prog
all postscript $(TARG).ps: $(SOURCE)
all: $(SOURCE)
pdflatex $(TARG).tex
pdflatex $(TARG).tex
pdflatex $(TARG).tex
postscript $(TARG).ps: $(SOURCE)
latex $(TARG).tex
latex $(TARG).tex
latex $(TARG).tex

52
doc/prog/cvsintro.tex
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@ -23,7 +23,7 @@ facilitated, allowing efficient and speedy resolution of conflicts.
This section provides a brief introduction and overview of the CVS system.
Developers needing more detailed information on specific CVS commands and
capabilities are refered to the on-line documentation included in the CVS
code package (i.e., the \verb+man+ pages; consult your system administrator
code package (i.e., the \texttt{man} pages; consult your system administrator
if your system does not have them installed.)
\subsection{Introduction to CVS}
@ -237,68 +237,68 @@ do anything. Honest.)
The following is provided as a quick reference guide to CVS. A more
detailed short-form reference is available in
\verb+nwchem/doc/cvshelp.man+. Detailed documentation can be obtained using
\texttt{nwchem/doc/cvshelp.man}. Detailed documentation can be obtained using
the command
\verb+man cvs+.
\texttt{man cvs}.
\begin{description}
\item{\verb+setenv CVSROOT /msrc/proj/mss+} --- in \verb+csh+ this
\item{\texttt{setenv CVSROOT /msrc/proj/mss}} --- in \texttt{csh} this
defines the path to the CVS repository. Put this in your
\verb+.cshrc+ or \verb+.mycshrc+.
\texttt{.cshrc} or \texttt{.mycshrc}.
\item{\verb+cvs co nwchem+} --- checks out the entire source for NWChem into
the directory \verb+nwchem+. The repository is unaffected.
\item{\texttt{cvs co nwchem}} --- checks out the entire source for NWChem into
the directory \texttt{nwchem}. The repository is unaffected.
\item{\verb+cvs -n update+} --- compares the contents of the current
\item{\texttt{cvs -n update}} --- compares the contents of the current
directory and all subdirectories against the repository and flags
files according to their status:
\begin{description}
\item{\verb+?+} --- the file is not maintained by CVS.
\item{\verb+M+} --- your checked-out version differs from the original
\item{\texttt{?}} --- the file is not maintained by CVS.
\item{\texttt{M}} --- your checked-out version differs from the original
(i.e., you edited it).
\item{\verb+U+} --- your checked-out version is out-of-date and
\item{\texttt{U}} --- your checked-out version is out-of-date and
needs updating.
\item{\verb+C+} --- potential conflict. You have changed this file
\item{\texttt{C}} --- potential conflict. You have changed this file
and the source in the repository has also changed.
\item{File not listed} --- your source is the same as that in the repository.
\end{description}
Neither the repository nor your source are changed.
\item{\verb+cvs update+} --- updates the contents of the current
\item{\texttt{cvs update}} --- updates the contents of the current
directory and all subdirectories with the latest versions of the
source, again flagging files according to their status. {\em You are
responsible for correcting files that CVS flags as containing
conflicts between edits you and others have made.} However, CVS
handles all other merging. New files will also be added to your
source, but to get new directories you must append the
\verb+-d+ flag. Your source is changed; the repository is
\texttt{-d} flag. Your source is changed; the repository is
unaffected.
\item{\verb+cvs diff filename+} --- generates differences between the
\item{\texttt{cvs diff filename}} --- generates differences between the
file and the version of the file you checked out (i.e., it indicates
edits you made). If you want to compare against the most recent
version in the repository use \verb+cvs diff -r head filename+.
version in the repository use \texttt{cvs diff -r head filename}.
Neither the repository nor your source are changed.
\item{\verb+cvs add filename+} --- adds a new file to the repository.
The new file is not actually added until you execute \verb+cvs
commit+. Changes CVS internal information in your source tree but
\item{\texttt{cvs add filename}} --- adds a new file to the repository.
The new file is not actually added until you execute \texttt{cvs
commit}. Changes CVS internal information in your source tree but
does not affect the repository.
\item{\verb+cvs rm filename+} --- to delete a file from the repository
delete it from your source with the standard UNIX \verb+rm+ command
\item{\texttt{cvs rm filename}} --- to delete a file from the repository
delete it from your source with the standard UNIX \texttt{rm} command
then tell CVS to delete it with this command. The file
is not actually removed until you execute \verb+cvs commit+. Changes CVS
is not actually removed until you execute \texttt{cvs commit}. Changes CVS
internal information in your source tree but does not affect the
repository.
\item{\verb+cvs commit+} --- this is the only command that affects the
\item{\texttt{cvs commit}} --- this is the only command that affects the
repository. Before committing changes and updating the repository
with changes in a list of files or the current directory tree you
must
\begin{itemize}
\item ensure that all of your sources are up-to-date with respect to
the repository by using \verb+cvs update+,
the repository by using \texttt{cvs update},
\item resolve all conflicts resulting from the update, and
\item ensure that the updated code functions correctly.
\end{itemize}
@ -317,10 +317,10 @@ the command
CVS version information is
"sticky". That is, CVS usually remembers the specific version checked out
to a working directory. This can be confusing,
since the output of such commands as \verb+cvs update+, etc., will not
since the output of such commands as \texttt{cvs update}, etc., will not
always refer to the latest (or
head) version. Changes can magically
disappear. This may be desirable. Or it may not be. The option \verb+-A+
disappear. This may be desirable. Or it may not be. The option \texttt{-A}
forces the system to look at the lastest version when doing the update.
The form of the command is

152
doc/prog/ecce.tex
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@ -51,7 +51,7 @@ The current version of NWChem includes output for
\item Geometry as input by the user
\item Geometry when updated by STEPPER or DRIVER
\item Name of basis set(s) used by the application (e.g., if {\tt ao
basis} was set to be \verb+6-31g*+)
basis} was set to be \texttt{6-31g*})
\item Convergence of SCF/DFT (energy and orbital-gradient norm)
\item Final converged total energies
\item Gradients w.r.t. geometry (analytic and numerical) and norm thereof
@ -78,16 +78,16 @@ the following general format was proposed,
\end{verbatim}
where:
\begin{description}
\item [\verb+<module stack>+] is a white space separated list of
\item [\texttt{<module stack>}] is a white space separated list of
module names representing the (logical) call tree,
\item [\verb+<dim1> ... <dimn>+] contains the size of each dimension
\item [\texttt{<dim1> ... <dimn>}] contains the size of each dimension
for arrays or tensors (unity for a scalar),
\item [\verb+<keyword>+] identifies the quantity that is being output
\item [\texttt{<keyword>}] identifies the quantity that is being output
(See below for more detail on the actual keywords.)
\item [\verb+<type>+] is the data type (\verb+"char"+, \verb+"int"+,
\verb+"long"+, \verb+"float"+, \verb+"double"+, \verb+"complex
float"+, and \verb+"logical"+),
\item [\verb+<data>+] contains the values (one character string per
\item [\texttt{<type>}] is the data type (\texttt{"char"}, \texttt{"int"},
\texttt{"long"}, \texttt{"float"}, \texttt{"double"}, \texttt{"complex
float"}, and \texttt{"logical"}),
\item [\texttt{<data>}] contains the values (one character string per
line, multiple values per line for other data types limited to circa
80 characters per line).
\end{description}
@ -124,7 +124,7 @@ If printing is enabled, prints
<module>
<module stack>%end%enter%1%character
\end{verbatim}
and then pushes \verb+<module>+ onto the module name stack.
and then pushes \texttt{<module>} onto the module name stack.
Module names will everywhere be printed with internal white space
replaced with underscores.
@ -147,8 +147,8 @@ If printing is enabled, prints
<module stack>%end%exit%2%character
\end{verbatim}
and (with the valid assumption that no nwchem module is reentrant)
pops the module name stack until either \verb+<module>+ is popped
off it, or the stack is empty. If \verb+<module>+ is not found on
pops the module name stack until either \texttt{<module>} is popped
off it, or the stack is empty. If \texttt{<module>} is not found on
the stack print an informative message to stderr (no more than
one such message per calculation) and continue.
@ -180,9 +180,9 @@ Print a 1-dimensional array of the specified type.
\begin{quotation}
Real data will be printed with the printf format \verb+%.14e+
Real data will be printed with the printf format \texttt{\%.14e}
Boolean data will be printed as \verb+t+ and \verb+f+
Boolean data will be printed as \texttt{t} and \texttt{f}
\end{quotation}
@ -234,7 +234,7 @@ arrays of character strings from C is not currently provided for).
void ecce_print_control(int status, int *old)
\end{verbatim}
Sets the boolean (0=FALSE, 1=TRUE) controling printing to \verb=status= and
Sets the boolean (0=FALSE, 1=TRUE) controling printing to \texttt{status} and
returns the previous setting.
\subsubsection{ routine ecce\_print\_file\_open(filename)}
@ -250,7 +250,7 @@ returns the previous setting.
other ecce routines, and continue.
Inside NWChem only process $0$ would open the file and all other
processes would therefore quietly ignore all \verb+ecce_*()+ calls.
processes would therefore quietly ignore all \texttt{ecce\_\*()} calls.
\subsubsection{ routine ecce\_print\_file\_close()}
@ -299,11 +299,11 @@ status. Some of these can be standardized, most probably cannot.
Standard exit status values include
\begin{description}
\item [\verb+"ok"+] --- success.
\item [\verb+"warning"+] --- success, but user should check the output for
\item [\texttt{"ok"}] --- success.
\item [\texttt{"warning"}] --- success, but user should check the output for
more information.
\item [\verb+"error"+] --- a fatal user or program error.
\item [\verb+"failed to converge"+] --- sometimes this is OK.
\item [\texttt{"error"}] --- a fatal user or program error.
\item [\texttt{"failed to converge"}] --- sometimes this is OK.
\end{description}
\subsection{Standard keywords}
@ -320,7 +320,7 @@ The NWChem electronic structure modules should output all quantities
in atomic units and leave it to Ecce to handle any necessary
conversions. Exceptions to this convention can be made, but a
distinct keyword should be used (perhaps including the actual units
used, e.g., \verb+"vibrational frequencies (cm-1)"+).
used, e.g., \texttt{"vibrational frequencies (cm-1)"}).
Here is the master list of keywords. All Ecce print keywords should
be registered here. (Note: not all keywords given by NWChem are used
@ -329,93 +329,93 @@ by Ecce. The ones listed below are those that NWChem uses.)
\subsubsection{Converged/final energies}
\begin{description}
\item [\verb+total energy+] --- the total energy at level of the module stack.
\item [\verb+mp2 energy+] --- the total MP2 energy.
\item [\verb+ccsd total energy+] --- the total ccsd energy.
\item [\verb+total ccsd energy+] --- the total ccsd energy.
\item [\verb+total ccsd(t) energy+] --- the total ccsd(t) energy.
\item [\verb+total ccsd+t(ccsd) energy+] --- the total ccsd+t(ccsd) energy.
\item [\verb+two-electron energy+] --- the two-electron energy
\item [\texttt{total energy}] --- the total energy at level of the module stack.
\item [\texttt{mp2 energy}] --- the total MP2 energy.
\item [\texttt{ccsd total energy}] --- the total ccsd energy.
\item [\texttt{total ccsd energy}] --- the total ccsd energy.
\item [\texttt{total ccsd(t) energy}] --- the total ccsd(t) energy.
\item [\texttt{total ccsd}t(ccsd) energy+] --- the total ccsd+t(ccsd) energy.
\item [\texttt{two-electron energy}] --- the two-electron energy
(Coulomb plus exchange).
\item [\verb+coulomb energy+] --- the (inter-electron) Coulomb
\item [\texttt{coulomb energy}] --- the (inter-electron) Coulomb
energy
\item [\verb+exchange energy+] --- the exchange energy.
\item [\verb+correlation energy+] --- the correlation energy
\item [\texttt{exchange energy}] --- the exchange energy.
\item [\texttt{correlation energy}] --- the correlation energy
(relative to the pertitnent SCF or MCSCF reference function), generally refers
to MP2 or DFT.
\item [\verb+ccsd correlation energy+] --- the CCSD correlation energy
\item [\texttt{ccsd correlation energy}] --- the CCSD correlation energy
(relative to the pertitnent SCF or MCSCF reference function).
\item [\verb+nuclear repulsion energy+] --- the nuclear repulsion
\item [\texttt{nuclear repulsion energy}] --- the nuclear repulsion
energy at the current geometry.
\item [\verb+zero point energy+] --- zero point energy from a frequency calculation.
\item [\texttt{zero point energy}] --- zero point energy from a frequency calculation.
\end{description}
\subsubsection{Converged/final properties}
\begin{description}
\item [\verb+geometry+] --- the current geometry of the molecule.
\item [\verb+cartesian coordinates+] --- the current cartesians of the molecule.
\item [\verb+gradients+] --- the current gradient of the molecule.
\item [\verb+total gradient+] --- the current gradient of the molecule.
\item [\verb+total dipole+] --- a 3--vector of $(x,y,z)$ dipole
\item [\texttt{geometry}] --- the current geometry of the molecule.
\item [\texttt{cartesian coordinates}] --- the current cartesians of the molecule.
\item [\texttt{gradients}] --- the current gradient of the molecule.
\item [\texttt{total gradient}] --- the current gradient of the molecule.
\item [\texttt{total dipole}] --- a 3--vector of $(x,y,z)$ dipole
moments.
\item [\verb+open shell dipole+] --- a 3--vector of $(x,y,z)$ dipole
\item [\texttt{open shell dipole}] --- a 3--vector of $(x,y,z)$ dipole
moments.
\item [\verb+alpha electronic dipole+] --- a 3--vector of $(x,y,z)$ dipole
\item [\texttt{alpha electronic dipole}] --- a 3--vector of $(x,y,z)$ dipole
moments.
\item [\verb+beta electronic dipole+] --- a 3--vector of $(x,y,z)$ dipole
\item [\texttt{beta electronic dipole}] --- a 3--vector of $(x,y,z)$ dipole
moments.
\item [\verb+nuclear dipole+] --- a 3--vector of $(x,y,z)$ dipole
\item [\texttt{nuclear dipole}] --- a 3--vector of $(x,y,z)$ dipole
moments.
\item [\verb+total quadrupole+] ---
\item [\verb+open shell quadrupole+] ---
\item [\verb+alpha electronic quadrupole+] ---
\item [\verb+beta electronic quadrupole+] ---
\item [\verb+nuclear quadrupole+] ---
\item [\verb+total mulliken atomic charges+] --- an $N_{atom}$--vector of the charge
\item [\texttt{total quadrupole}] ---
\item [\texttt{open shell quadrupole}] ---
\item [\texttt{alpha electronic quadrupole}] ---
\item [\texttt{beta electronic quadrupole}] ---
\item [\texttt{nuclear quadrupole}] ---
\item [\texttt{total mulliken atomic charges}] --- an $N_{atom}$--vector of the charge
assigned by the Mulliken analysis to each atom.
\item [\verb+total mulliken shell charges+] --- an $N_{shell}$--vector of
\item [\texttt{total mulliken shell charges}] --- an $N_{shell}$--vector of
the charge assigned by the Mulliken analysis to each shell of basis
functions.
\item [\verb+orbital symmetries+] --- symmetry information for each molecular
\item [\texttt{orbital symmetries}] --- symmetry information for each molecular
orbital.
\item [\verb+orbital energies+] --- orbital energies for each molecular orbital.
\item [\verb+frequencies+] --- frequencies.
\item [\verb+projected frequencies+] --- projected frequencies.
\item [\verb+normal modes+] --- normal modes associated with each frequency.
\item [\verb+projected normal modes+] --- projected normal modes associated
\item [\texttt{orbital energies}] --- orbital energies for each molecular orbital.
\item [\texttt{frequencies}] --- frequencies.
\item [\texttt{projected frequencies}] --- projected frequencies.
\item [\texttt{normal modes}] --- normal modes associated with each frequency.
\item [\texttt{projected normal modes}] --- projected normal modes associated
with each frequency.
\item [\verb+intensities+] --- frequency intensities.
\item [\verb+intensities+] --- frequency intensities.
\item [\verb+intensities (debye/ang)2+] --- frequency intensities in (debye/ang)2.
\item [\verb+intensities (KM/mol)+] --- frequency intensities in (KM/mol).
\item [\verb+projected intensities+] --- frequency projected intensities.
\item [\verb+projected intensities (debye/ang)2+] --- frequency projected intensities
\item [\texttt{intensities}] --- frequency intensities.
\item [\texttt{intensities}] --- frequency intensities.
\item [\texttt{intensities (debye/ang)2}] --- frequency intensities in (debye/ang)2.
\item [\texttt{intensities (KM/mol)}] --- frequency intensities in (KM/mol).
\item [\texttt{projected intensities}] --- frequency projected intensities.
\item [\texttt{projected intensities (debye/ang)2}] --- frequency projected intensities
in (debye/ang)2.
\item [\verb+projected intensities (KM/mol)+] --- frequency projected intensities
\item [\texttt{projected intensities (KM/mol)}] --- frequency projected intensities
in (KM/mol).
\end{description}
\subsubsection{Convergence information}
\begin{description}
\item [\verb+iteration+] --- the iteration number for geometry steps, starting at 1.
\item [\verb+iteration counter+] --- the iteration counter when optimizing the
\item [\texttt{iteration}] --- the iteration number for geometry steps, starting at 1.
\item [\texttt{iteration counter}] --- the iteration counter when optimizing the
wavefunction.
\item [\verb+iterative total energy difference+] --- the change in the total
\item [\texttt{iterative total energy difference}] --- the change in the total
energy since the previous iteration.
\item [\verb+gradient norm+] --- an (estimate) of the norm of the
\item [\texttt{gradient norm}] --- an (estimate) of the norm of the
gradient vector or something proportional to it for
minimization/transition state algorithms (e.g., SCF
orbital-gradient, DFT norm of occupied-virtual Fock-matrix, geometry
optimization cartesian nuclear gradient).
\item [\verb+gradient max+] --- an (estimate) of the maximum absolute
\item [\texttt{gradient max}] --- an (estimate) of the maximum absolute
value element in the gradient vector.
\item [\verb+residual norm+] --- norm of the error vector in
\item [\texttt{residual norm}] --- norm of the error vector in
linear/non-linear equation solution
\item [\verb+residual max+] --- the absolute maximum value of the
\item [\texttt{residual max}] --- the absolute maximum value of the
residual vector
\item [\verb+scaled residual norm+] --- the norm of the residual
\item [\texttt{scaled residual norm}] --- the norm of the residual
scaled by the norm of the RHS vector in the iterative solution of
non-linear equations (roughly the negative logarithm of the number of
significant figures)
@ -444,11 +444,11 @@ does not do what you want then it can be extended.
Additional keywords:
\begin{description}
\item [\verb+all tasks cpu time+] ---
\item [\verb+single task cpu time+] ---
\item [\verb+cpu time+] ---
\item [\verb+all tasks wall time+] ---
\item [\verb+single task wall time+] ---
\item [\verb+wall time+] ---
\item [\texttt{all tasks cpu time}] ---
\item [\texttt{single task cpu time}] ---
\item [\texttt{cpu time}] ---
\item [\texttt{all tasks wall time}] ---
\item [\texttt{single task wall time}] ---
\item [\texttt{wall time}] ---
\end{description}

2
doc/prog/nwarch.tex
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@ -235,7 +235,7 @@ the basis set object (see Section \ref{sec:basis}), the
linear algebra routines (see Section \ref{sec:la}),
symmetry (see Section \ref{sec:sym}, and
the integral API (see Section
\ref{sec:intapi}). Each of these
\ref{appendix_intapi}). Each of these
tools provides a basic functionality that is common to many of the
algorithms in chemistry. The integral API provides a common interface to
the three integral packages available in NWChem. The basis set object

14
doc/prog/prog.tex
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@ -1,9 +1,17 @@
% $Id$
\documentstyle[fullpage,12pt,fleqn]{book}
%\documentstyle[fullpage,12pt,fleqn]{book}
\documentclass{book}
\setlength{\parskip}{6pt}
\usepackage{fullpage}
\usepackage{fleqn}
\usepackage[utf8]{inputenc}
\usepackage{textcomp}
\usepackage{mathptmx}
\usepackage{amsmath}
\usepackage{amssymb}
\newcommand{\TRUE}{\verb+.true.+}
\newcommand{\FALSE}{\verb+.false.+}
\newcommand{\TRUE}{\texttt{.true.}}
\newcommand{\FALSE}{\texttt{.false.}}
\newcommand{\nwchemversion}{5.1.1}
\newcommand{\nwchemyear}{2008}