NWChem/web/doc/user.4.6/node36.html
2006-01-12 21:22:32 +00:00

457 lines
14 KiB
HTML

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
patched version by: Kenshi Muto, Debian Project.
LaTeX2HTML 2002 (1.62),
original version by: Nikos Drakos, CBLU, University of Leeds
* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
* with significant contributions from:
Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
<HTML>
<HEAD>
<TITLE>34. File formats</TITLE>
<META NAME="description" CONTENT="34. File formats">
<META NAME="keywords" CONTENT="user">
<META NAME="resource-type" CONTENT="document">
<META NAME="distribution" CONTENT="global">
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
<LINK REL="STYLESHEET" HREF="user.css">
<LINK REL="next" HREF="node37.html">
<LINK REL="previous" HREF="node35.html">
<LINK REL="up" HREF="user.html">
<LINK REL="next" HREF="node37.html">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<!--Navigation Panel-->
<A NAME="tex2html1679"
HREF="node37.html">
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A>
<A NAME="tex2html1675"
HREF="user.html">
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A>
<A NAME="tex2html1669"
HREF="node35.html">
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A>
<A NAME="tex2html1677"
HREF="node2.html">
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="contents.png"></A>
<BR>
<B> Next:</B> <A NAME="tex2html1680"
HREF="node37.html">35. Pseudopotential plane-wave density</A>
<B> Up:</B> <A NAME="tex2html1676"
HREF="user.html">user</A>
<B> Previous:</B> <A NAME="tex2html1670"
HREF="node35.html">33. Combined quantum and</A>
&nbsp <B> <A NAME="tex2html1678"
HREF="node2.html">Contents</A></B>
<BR>
<BR>
<!--End of Navigation Panel-->
<H1><A NAME="SECTION003600000000000000000">
34. File formats</A>
</H1>
<A NAME="sec:formats"></A>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="9782"></A>
<TABLE>
<CAPTION><STRONG>Table 34.1:</STRONG>
The format of fragment files.</CAPTION>
<TR><TD>
<DIV ALIGN="CENTER">
<TABLE CELLPADDING=3 BORDER="1" ALIGN="CENTER">
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>Card</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>Format</TD>
<TD ALIGN="LEFT">Description</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>I-1-1</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>a1</TD>
<TD ALIGN="LEFT">$ to identify the start of a fragment</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>I-1-2</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>a10</TD>
<TD ALIGN="LEFT">name of the fragment, the tenth character</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">N: identifies beginning of a chain</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">C: identifies end of a chain</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">blank: identifies chain fragment</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">M: identifies an integral molecule</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>I-2-1</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>i5</TD>
<TD ALIGN="LEFT">number of atoms in the fragment</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43><B>For each atom one deck II</B></TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">&nbsp;</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-1</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>i5</TD>
<TD ALIGN="LEFT">atom sequence number</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-2</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>a6</TD>
<TD ALIGN="LEFT">atom name</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-3</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>a5</TD>
<TD ALIGN="LEFT">atom type</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-4</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>a1</TD>
<TD ALIGN="LEFT">dynamics type</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT"><code> </code> : normal</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT"><code>D</code> : dummy atom</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT"><code>S</code> : solute interactions only</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT"><code>Q</code> : quantum atom</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">other : intramolecular solute interactions only</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-5</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>i5</TD>
<TD ALIGN="LEFT">link number</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">0: no link</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">1: first atom in chain</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">2: second atom in chain</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">3 and up: other links</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-6</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>i5</TD>
<TD ALIGN="LEFT">environment type</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">0: no special identifier</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">1: planar, using improper torsion</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">2: tetrahedral, using improper torsion</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">3: tetrahedral, using improper torsion</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>&nbsp;</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">4: atom in aromatic ring</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-7</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>i5</TD>
<TD ALIGN="LEFT">charge group</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-8</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>i5</TD>
<TD ALIGN="LEFT">polarization group</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-9</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>f12.6</TD>
<TD ALIGN="LEFT">atomic partial charge</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>II-1-10</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>f12.6</TD>
<TD ALIGN="LEFT">atomic polarizability</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43><B>Any number of cards in deck III to specify complete
connectivity</B></TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>&nbsp;</TD>
<TD ALIGN="LEFT">&nbsp;</TD>
</TR>
<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=43>III-1-1</TD>
<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=34>16i5</TD>
<TD ALIGN="LEFT">connectivity, duplication allowed</TD>
</TR>
</TABLE>
</DIV></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdseg1"></A><A NAME="9784"></A>
<TABLE>
<CAPTION><STRONG>Table 34.2:</STRONG>
Segment file format, table 1 of 6.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="235" BORDER="0"
SRC="img247.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...mproper dihedrals in the segment\\
\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdseg2"></A><A NAME="9786"></A>
<TABLE>
<CAPTION><STRONG>Table 34.3:</STRONG>
Segment file format, table 2 of 6.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="770" BORDER="0"
SRC="img248.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...\pi\epsilon_o$\ in nm$^3$, set 3\\
\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdseg3"></A><A NAME="9788"></A>
<TABLE>
<CAPTION><STRONG>Table 34.4:</STRONG>
Segment file format, table 3 of 6.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="330" BORDER="0"
SRC="img249.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...in kJ nm$^2$\ mol$^{-1}$, set 3 \\
\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdseg4"></A><A NAME="9790"></A>
<TABLE>
<CAPTION><STRONG>Table 34.5:</STRONG>
Segment file format, table 4 of 6.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="330" BORDER="0"
SRC="img250.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...onstant in kJ mol$^{-1}$, set 3 \\
\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdseg5"></A><A NAME="9792"></A>
<TABLE>
<CAPTION><STRONG>Table 34.6:</STRONG>
Segment file format, table 5 of 6.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="407" BORDER="0"
SRC="img251.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...onstant in kJ mol$^{-1}$, set 3 \\
\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdseg6"></A><A NAME="9794"></A>
<TABLE>
<CAPTION><STRONG>Table 34.7:</STRONG>
Segment file format, table 6 of 6.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="353" BORDER="0"
SRC="img252.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...t in kJ mol$^{-1}$, set 3 \\
\hline\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdseq"></A><A NAME="9796"></A>
<TABLE>
<CAPTION><STRONG>Table 34.8:</STRONG>
Sequence file format.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="397" BORDER="0"
SRC="img253.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...II to specify the system} \\
\hline\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdtrj"></A><A NAME="9798"></A>
<TABLE>
<CAPTION><STRONG>Table 34.9:</STRONG>
Trajectory file format.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="822" BORDER="0"
SRC="img254.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...e atom velocities, if lvs \\
\hline\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdgib"></A><A NAME="9800"></A>
<TABLE>
<CAPTION><STRONG>Table 34.10:</STRONG>
Free energy file format.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="240" BORDER="0"
SRC="img255.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...rgy at current $\lambda$\ \\
\hline\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdrms"></A><A NAME="9802"></A>
<TABLE>
<CAPTION><STRONG>Table 34.11:</STRONG>
Root mean square deviation file format.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="356" BORDER="0"
SRC="img256.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...ion after superimposition \\
\hline\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<BR><P></P>
<DIV ALIGN="CENTER"><A NAME="tbl:nwmdprp"></A><A NAME="9804"></A>
<TABLE>
<CAPTION><STRONG>Table 34.12:</STRONG>
Property file format.</CAPTION>
<TR><TD><IMG
WIDTH="680" HEIGHT="145" BORDER="0"
SRC="img257.gif"
ALT="\begin{table}\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hlin...
...12.5) &amp; value of property \\
\hline\hline
\end{tabular*}\end{center}\end{table}"></TD></TR>
</TABLE>
</DIV><P></P>
<BR>
<P>
<HR>
<!--Navigation Panel-->
<A NAME="tex2html1679"
HREF="node37.html">
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A>
<A NAME="tex2html1675"
HREF="user.html">
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A>
<A NAME="tex2html1669"
HREF="node35.html">
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A>
<A NAME="tex2html1677"
HREF="node2.html">
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="contents.png"></A>
<BR>
<B> Next:</B> <A NAME="tex2html1680"
HREF="node37.html">35. Pseudopotential plane-wave density</A>
<B> Up:</B> <A NAME="tex2html1676"
HREF="user.html">user</A>
<B> Previous:</B> <A NAME="tex2html1670"
HREF="node35.html">33. Combined quantum and</A>
&nbsp <B> <A NAME="tex2html1678"
HREF="node2.html">Contents</A></B>
<!--End of Navigation Panel-->
<ADDRESS>
Edoardo Apra
2004-05-25
</ADDRESS>
</BODY>
</HTML>