comp-chem/NWChem
1
0
Fork 0
mirror of https://github.com/nwchemgit/nwchem.git synced 2026-07-29 06:35:39 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions 1

Add center and rotate documentation

Browse source
This commit is contained in:
Tjerk Straatsma 2001-07-17 22:37:16 +00:00
parent 51701118b3
commit 8c7241b366
1 changed files with 29 additions and 6 deletions
Download patch file Download diff file Expand all files Collapse all files

35
doc/user/analysis.tex
View file

@ -116,9 +116,24 @@ back into the box according to the periodic boundary conditions.
The directive for this operation is
\begin{verbatim}
center [<integer imol>]
center <integer imol> [<integer jmol default imol>]
\end{verbatim}
Coordinates of each frame read from a trajectory file can be
rotated using
\begin{verbatim}
rotate ( off | x | y | z ) <real angle units degrees>
\end{verbatim}
If \verb+center+ was defined, rotation takes place after
the system has been centered. The \verb+rotate+ directives
only apply to frames read from the trajectory files, and not
to the reference coordinates. Upto 100 \verb+rotate+ directives
can be specified, which will be carried out in the order in which
they appear in the input deck. \verb+rotate off+ cancels all
previously defined \verb+rotate+ directives.
To set hydrogen bond criteria:
\begin{verbatim}
@ -129,11 +144,12 @@ hbond [distance [[<real rhbmin default 0.0>] <real rhbmin>]] \
\section{Selection}
Analyses can be applied to a selection of solute atoms. The selection
is determined by
Analyses can be applied to a selection of solute atoms and solvent molecules.
The selection is determined by
\begin{verbatim}
select [ <integer isgm> [ <integer jsgm> ]] [ { <string atom> } ]
select ( [ <integer isgm> [ <integer jsgm> ]] [ { <string atom> } ] |
solvent <real range> | save <string filename> | read <string filename> )
\end{verbatim}
where {\rm isgm} is the first segment number, {\rm jsgm} is the last
@ -166,6 +182,9 @@ select solvent <real range>
After solvent selection, the solute atom selection is reset to being all
selected.
The current selection can be saved to, or read from a file using the
\verb+save+ and \verb+read+ keywords, respectively.
\par
Some analysis are performed on groups of atoms. These groups of atoms
@ -316,16 +335,20 @@ To copy the selected frames from the specified trejctory file(s),
onto a new file, use
\begin{verbatim}
copy [solute] <string filename>
copy [solute] [rotate <real tangle>] <string filename>
\end{verbatim}
To superimpose the selected atoms for each specified frame to the
reference coordinates before copying onto a new file, use
\begin{verbatim}
super [solute] <string filename>
super [solute] [rotate <real tangle>] <string filename>
\end{verbatim}
The \verb+rotate+ directive specifies that the structure will make
a full ratation every tangle ps. This directive only has effect when
writing povray files.
The format of the new file is determined from the extension, which
can be one of