mirror of
https://github.com/nwchemgit/nwchem.git
synced 2026-07-21 06:25:21 -04:00
updates [ci skip]
This commit is contained in:
edoapra
parent
d9305f3e44
commit
db06ad8e8c
5 changed files with 119 additions and 107 deletions
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@ -25,7 +25,11 @@
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TARG = prog
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all postscript $(TARG).ps: $(SOURCE)
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all: $(SOURCE)
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pdflatex $(TARG).tex
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pdflatex $(TARG).tex
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pdflatex $(TARG).tex
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postscript $(TARG).ps: $(SOURCE)
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latex $(TARG).tex
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latex $(TARG).tex
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latex $(TARG).tex
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@ -23,7 +23,7 @@ facilitated, allowing efficient and speedy resolution of conflicts.
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This section provides a brief introduction and overview of the CVS system.
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Developers needing more detailed information on specific CVS commands and
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capabilities are refered to the on-line documentation included in the CVS
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code package (i.e., the \verb+man+ pages; consult your system administrator
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code package (i.e., the \texttt{man} pages; consult your system administrator
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if your system does not have them installed.)
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\subsection{Introduction to CVS}
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@ -237,68 +237,68 @@ do anything. Honest.)
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The following is provided as a quick reference guide to CVS. A more
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detailed short-form reference is available in
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\verb+nwchem/doc/cvshelp.man+. Detailed documentation can be obtained using
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\texttt{nwchem/doc/cvshelp.man}. Detailed documentation can be obtained using
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the command
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\verb+man cvs+.
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\texttt{man cvs}.
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\begin{description}
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\item{\verb+setenv CVSROOT /msrc/proj/mss+} --- in \verb+csh+ this
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\item{\texttt{setenv CVSROOT /msrc/proj/mss}} --- in \texttt{csh} this
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defines the path to the CVS repository. Put this in your
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\verb+.cshrc+ or \verb+.mycshrc+.
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\texttt{.cshrc} or \texttt{.mycshrc}.
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\item{\verb+cvs co nwchem+} --- checks out the entire source for NWChem into
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the directory \verb+nwchem+. The repository is unaffected.
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\item{\texttt{cvs co nwchem}} --- checks out the entire source for NWChem into
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the directory \texttt{nwchem}. The repository is unaffected.
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\item{\verb+cvs -n update+} --- compares the contents of the current
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\item{\texttt{cvs -n update}} --- compares the contents of the current
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directory and all subdirectories against the repository and flags
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files according to their status:
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\begin{description}
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\item{\verb+?+} --- the file is not maintained by CVS.
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\item{\verb+M+} --- your checked-out version differs from the original
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\item{\texttt{?}} --- the file is not maintained by CVS.
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\item{\texttt{M}} --- your checked-out version differs from the original
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(i.e., you edited it).
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\item{\verb+U+} --- your checked-out version is out-of-date and
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\item{\texttt{U}} --- your checked-out version is out-of-date and
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needs updating.
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\item{\verb+C+} --- potential conflict. You have changed this file
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\item{\texttt{C}} --- potential conflict. You have changed this file
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and the source in the repository has also changed.
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\item{File not listed} --- your source is the same as that in the repository.
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\end{description}
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Neither the repository nor your source are changed.
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\item{\verb+cvs update+} --- updates the contents of the current
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\item{\texttt{cvs update}} --- updates the contents of the current
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directory and all subdirectories with the latest versions of the
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source, again flagging files according to their status. {\em You are
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responsible for correcting files that CVS flags as containing
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conflicts between edits you and others have made.} However, CVS
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handles all other merging. New files will also be added to your
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source, but to get new directories you must append the
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\verb+-d+ flag. Your source is changed; the repository is
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\texttt{-d} flag. Your source is changed; the repository is
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unaffected.
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\item{\verb+cvs diff filename+} --- generates differences between the
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\item{\texttt{cvs diff filename}} --- generates differences between the
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file and the version of the file you checked out (i.e., it indicates
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edits you made). If you want to compare against the most recent
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version in the repository use \verb+cvs diff -r head filename+.
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version in the repository use \texttt{cvs diff -r head filename}.
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Neither the repository nor your source are changed.
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\item{\verb+cvs add filename+} --- adds a new file to the repository.
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The new file is not actually added until you execute \verb+cvs
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commit+. Changes CVS internal information in your source tree but
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\item{\texttt{cvs add filename}} --- adds a new file to the repository.
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The new file is not actually added until you execute \texttt{cvs
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commit}. Changes CVS internal information in your source tree but
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does not affect the repository.
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\item{\verb+cvs rm filename+} --- to delete a file from the repository
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delete it from your source with the standard UNIX \verb+rm+ command
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\item{\texttt{cvs rm filename}} --- to delete a file from the repository
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delete it from your source with the standard UNIX \texttt{rm} command
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then tell CVS to delete it with this command. The file
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is not actually removed until you execute \verb+cvs commit+. Changes CVS
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is not actually removed until you execute \texttt{cvs commit}. Changes CVS
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internal information in your source tree but does not affect the
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repository.
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\item{\verb+cvs commit+} --- this is the only command that affects the
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\item{\texttt{cvs commit}} --- this is the only command that affects the
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repository. Before committing changes and updating the repository
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with changes in a list of files or the current directory tree you
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must
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\begin{itemize}
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\item ensure that all of your sources are up-to-date with respect to
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the repository by using \verb+cvs update+,
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the repository by using \texttt{cvs update},
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\item resolve all conflicts resulting from the update, and
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\item ensure that the updated code functions correctly.
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\end{itemize}
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@ -317,10 +317,10 @@ the command
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CVS version information is
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"sticky". That is, CVS usually remembers the specific version checked out
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to a working directory. This can be confusing,
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since the output of such commands as \verb+cvs update+, etc., will not
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since the output of such commands as \texttt{cvs update}, etc., will not
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always refer to the latest (or
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head) version. Changes can magically
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disappear. This may be desirable. Or it may not be. The option \verb+-A+
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disappear. This may be desirable. Or it may not be. The option \texttt{-A}
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forces the system to look at the lastest version when doing the update.
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The form of the command is
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@ -51,7 +51,7 @@ The current version of NWChem includes output for
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\item Geometry as input by the user
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\item Geometry when updated by STEPPER or DRIVER
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\item Name of basis set(s) used by the application (e.g., if {\tt ao
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basis} was set to be \verb+6-31g*+)
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basis} was set to be \texttt{6-31g*})
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\item Convergence of SCF/DFT (energy and orbital-gradient norm)
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\item Final converged total energies
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\item Gradients w.r.t. geometry (analytic and numerical) and norm thereof
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@ -78,16 +78,16 @@ the following general format was proposed,
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\end{verbatim}
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where:
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\begin{description}
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\item [\verb+<module stack>+] is a white space separated list of
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\item [\texttt{<module stack>}] is a white space separated list of
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module names representing the (logical) call tree,
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\item [\verb+<dim1> ... <dimn>+] contains the size of each dimension
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\item [\texttt{<dim1> ... <dimn>}] contains the size of each dimension
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for arrays or tensors (unity for a scalar),
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\item [\verb+<keyword>+] identifies the quantity that is being output
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\item [\texttt{<keyword>}] identifies the quantity that is being output
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(See below for more detail on the actual keywords.)
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\item [\verb+<type>+] is the data type (\verb+"char"+, \verb+"int"+,
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\verb+"long"+, \verb+"float"+, \verb+"double"+, \verb+"complex
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float"+, and \verb+"logical"+),
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\item [\verb+<data>+] contains the values (one character string per
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\item [\texttt{<type>}] is the data type (\texttt{"char"}, \texttt{"int"},
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\texttt{"long"}, \texttt{"float"}, \texttt{"double"}, \texttt{"complex
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float"}, and \texttt{"logical"}),
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\item [\texttt{<data>}] contains the values (one character string per
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line, multiple values per line for other data types limited to circa
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80 characters per line).
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\end{description}
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@ -124,7 +124,7 @@ If printing is enabled, prints
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<module>
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<module stack>%end%enter%1%character
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\end{verbatim}
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and then pushes \verb+<module>+ onto the module name stack.
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and then pushes \texttt{<module>} onto the module name stack.
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Module names will everywhere be printed with internal white space
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replaced with underscores.
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@ -147,8 +147,8 @@ If printing is enabled, prints
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<module stack>%end%exit%2%character
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\end{verbatim}
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and (with the valid assumption that no nwchem module is reentrant)
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pops the module name stack until either \verb+<module>+ is popped
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off it, or the stack is empty. If \verb+<module>+ is not found on
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pops the module name stack until either \texttt{<module>} is popped
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off it, or the stack is empty. If \texttt{<module>} is not found on
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the stack print an informative message to stderr (no more than
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one such message per calculation) and continue.
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@ -180,9 +180,9 @@ Print a 1-dimensional array of the specified type.
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\begin{quotation}
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Real data will be printed with the printf format \verb+%.14e+
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Real data will be printed with the printf format \texttt{\%.14e}
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|
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Boolean data will be printed as \verb+t+ and \verb+f+
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Boolean data will be printed as \texttt{t} and \texttt{f}
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\end{quotation}
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@ -234,7 +234,7 @@ arrays of character strings from C is not currently provided for).
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void ecce_print_control(int status, int *old)
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\end{verbatim}
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Sets the boolean (0=FALSE, 1=TRUE) controling printing to \verb=status= and
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Sets the boolean (0=FALSE, 1=TRUE) controling printing to \texttt{status} and
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returns the previous setting.
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|
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\subsubsection{ routine ecce\_print\_file\_open(filename)}
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@ -250,7 +250,7 @@ returns the previous setting.
|
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other ecce routines, and continue.
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|
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Inside NWChem only process $0$ would open the file and all other
|
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processes would therefore quietly ignore all \verb+ecce_*()+ calls.
|
||||
processes would therefore quietly ignore all \texttt{ecce\_\*()} calls.
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||||
|
||||
\subsubsection{ routine ecce\_print\_file\_close()}
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||||
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@ -299,11 +299,11 @@ status. Some of these can be standardized, most probably cannot.
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Standard exit status values include
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||||
|
||||
\begin{description}
|
||||
\item [\verb+"ok"+] --- success.
|
||||
\item [\verb+"warning"+] --- success, but user should check the output for
|
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\item [\texttt{"ok"}] --- success.
|
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\item [\texttt{"warning"}] --- success, but user should check the output for
|
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more information.
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\item [\verb+"error"+] --- a fatal user or program error.
|
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\item [\verb+"failed to converge"+] --- sometimes this is OK.
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\item [\texttt{"error"}] --- a fatal user or program error.
|
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\item [\texttt{"failed to converge"}] --- sometimes this is OK.
|
||||
\end{description}
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\subsection{Standard keywords}
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@ -320,7 +320,7 @@ The NWChem electronic structure modules should output all quantities
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in atomic units and leave it to Ecce to handle any necessary
|
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conversions. Exceptions to this convention can be made, but a
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distinct keyword should be used (perhaps including the actual units
|
||||
used, e.g., \verb+"vibrational frequencies (cm-1)"+).
|
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used, e.g., \texttt{"vibrational frequencies (cm-1)"}).
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|
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Here is the master list of keywords. All Ecce print keywords should
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be registered here. (Note: not all keywords given by NWChem are used
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@ -329,93 +329,93 @@ by Ecce. The ones listed below are those that NWChem uses.)
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\subsubsection{Converged/final energies}
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|
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\begin{description}
|
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\item [\verb+total energy+] --- the total energy at level of the module stack.
|
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\item [\verb+mp2 energy+] --- the total MP2 energy.
|
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\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.
|
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\item [\verb+total ccsd+t(ccsd) energy+] --- the total ccsd+t(ccsd) energy.
|
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\item [\verb+two-electron energy+] --- the two-electron energy
|
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\item [\texttt{total energy}] --- the total energy at level of the module stack.
|
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\item [\texttt{mp2 energy}] --- the total MP2 energy.
|
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\item [\texttt{ccsd total energy}] --- the total ccsd energy.
|
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\item [\texttt{total ccsd energy}] --- the total ccsd energy.
|
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\item [\texttt{total ccsd(t) energy}] --- the total ccsd(t) energy.
|
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\item [\texttt{total ccsd}t(ccsd) energy+] --- the total ccsd+t(ccsd) energy.
|
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\item [\texttt{two-electron energy}] --- the two-electron energy
|
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(Coulomb plus exchange).
|
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\item [\verb+coulomb energy+] --- the (inter-electron) Coulomb
|
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\item [\texttt{coulomb energy}] --- the (inter-electron) Coulomb
|
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energy
|
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\item [\verb+exchange energy+] --- the exchange energy.
|
||||
\item [\verb+correlation energy+] --- the correlation energy
|
||||
\item [\texttt{exchange energy}] --- the exchange energy.
|
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\item [\texttt{correlation energy}] --- the correlation energy
|
||||
(relative to the pertitnent SCF or MCSCF reference function), generally refers
|
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to MP2 or DFT.
|
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\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).
|
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\item [\verb+nuclear repulsion energy+] --- the nuclear repulsion
|
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\item [\texttt{nuclear repulsion energy}] --- the nuclear repulsion
|
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energy at the current geometry.
|
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\item [\verb+zero point energy+] --- zero point energy from a frequency calculation.
|
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\item [\texttt{zero point energy}] --- zero point energy from a frequency calculation.
|
||||
\end{description}
|
||||
|
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\subsubsection{Converged/final properties}
|
||||
|
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\begin{description}
|
||||
\item [\verb+geometry+] --- the current geometry of the molecule.
|
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\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.
|
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\item [\texttt{gradients}] --- the current gradient of the molecule.
|
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\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.
|
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\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.
|
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\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}
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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}
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue