updates [ci skip]

doc/prog/GNUmakefile

@@ -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

doc/prog/cvsintro.tex

@@ -23,7 +23,7 @@ \section{Managing NWChem}
 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 @@ \subsection{Summary of CVS commands}
 
 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-  \item{\verb+U+} --- your checked-out version is out-of-date and
+  \item{\texttt{U}} --- your checked-out version is out-of-date and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 @@ \subsection{Troubleshooting CVS}
 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
 

doc/prog/ecce.tex

@@ -51,7 +51,7 @@ \subsection{Contents of Output for Ecce}
 \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 @@ \subsection{Format of Output}
 \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 @@ \subsubsection{  routine ecce\_print\_module\_entry(module)}
     <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 @@ \subsubsection{routine ecce\_print\_module\_exit(module, status)}
     <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 @@ \subsubsection{ routine ecce\_print1(keyword, ma\_type, data, dim1) }
 
     \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 @@ \subsubsection{routine ecce\_print\_control(status, old)}
      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 @@ \subsubsection{  routine ecce\_print\_file\_open(filename)}
     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 @@ \subsection{Standard exit status}
 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 @@ \subsection{Standard keywords}
 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 @@ \subsection{Standard keywords}
 \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 @@ \subsubsection{Timing and performance information}
 
 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}