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This commit is contained in:
Eric Bylaska
parent
86ed47b7d2
commit
0106497a86
3 changed files with 36 additions and 26 deletions
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@ -161,7 +161,7 @@ foreach document ($1)
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echo "htmlize: Compressing copies of postscript source"
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foreach file (${document}*.ps)
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if (-e $file) then
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compress < $file > ${document}/${file}.Z
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gzip < $file > ${document}/${file}.gz
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@ compress_stat += $status
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endif
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end
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@ -1,12 +1,12 @@
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%
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% $Id: fileformats.tex,v 1.6 2006-09-28 14:36:53 d3j191 Exp $
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% $Id: fileformats.tex,v 1.7 2007-04-10 23:43:18 bylaska Exp $
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%
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\label{sec:formats}
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%\section {Format fragment file}
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\section {Format fragment file}
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\begin{table}[h]
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\begin{center}
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\begin{tabular}{p{15mm}p{12mm}l}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Card & Format & Description \\ \hline
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I-1-1 & a1 & \$ to identify the start of a fragment \\ % $ for emacs
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@ -53,7 +53,7 @@ II-1-9 & i5 & polarization group\\
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II-1-10 & f12.6 & atomic partial charge\\
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II-1-11 & f12.6 & atomic polarizability\\
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\hline
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\mc{3}{l}{For each additional parameter set on card II-2}\\
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For each additional parameter set on card II-2\\
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\hline
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II-2-1 & 11x,a6 & atom type\\
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II-2-2 & a1 & dynamics type\\
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@ -70,9 +70,9 @@ connectivity} \\
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\hline
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III-1-1 & 16i5 & connectivity, duplication allowed\\
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\hline
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\mc{3}{l}{One blanc card to signal the end of the connectivity list}\\
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One blanc card to signal the end of the connectivity list\\
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\hline
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\mc{3}{l}{For each z-matrix definition one card IV}\\
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For each z-matrix definition one card IV\\
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\hline
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IV-1-1 & i5 & atom i \\
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IV-1-2 & i5 & atom j \\
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@ -82,12 +82,12 @@ IV-1-5 & f12.6 & bond length i-j\\
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IV-1-6 & f12.6 & angle i-j-k\\
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IV-1-7 & f12.6 & torson i-j-k-l\\
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\hline\hline
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\end{tabular}
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\end{tabular*}
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\caption{The format of fragment files.\label{tbl:nwmdfrg}}
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\end{center}
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\end{table}
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%\section {Format segment file}
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\section {Format segment file}
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\begin{table}[h]
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\begin{center}
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@ -112,7 +112,7 @@ I-3-6 & i5 & number of z-matrix definitions\\
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I-3-7 & i5 & number of parameter sets \\
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1-3-8 & i5 & default parameter set\\
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\hline
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\mc{3}{l}{For each prarmeter set one card I-4}\\
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For each prarmeter set one card I-4\\
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\hline
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I-4-1 & f12.6 & dipole correction energy \\
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\hline
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@ -141,7 +141,7 @@ II-1-5 & i5 & \\
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II-1-6 & i5 & charge group\\
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II-1-7 & i5 & polarization group\\
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\hline
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\mc{3}{l}{For each parameter set one card II-2}\\
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For each parameter set one card II-2\\
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\hline
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II-2-1 & 5x,a5 & atom type \\
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II-2-2 & a1 & dynamics type\\
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@ -174,7 +174,7 @@ III-1-5 & i5 & bond parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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\mc{3}{l}{For each parameter set one card III-2}\\
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For each parameter set one card III-2\\
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\hline
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III-2-1 & f12.6 & bond length in nm\\
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III-2-2 & e12.5 & bond force constant in kJ nm$^2$ mol$^{-1}$\\
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@ -200,7 +200,7 @@ IV-1-6 & i5 & angle parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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\mc{3}{l}{For each parameter set one card IV-2}\\
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For each parameter set one card IV-2\\
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\hline
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IV-2-1 & f10.6 & angle in radians\\
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IV-2-2 & e12.5 & angle force constant in kJ mol$^{-1}$\\
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@ -227,7 +227,7 @@ V-1-7 & i5 & proper dihedral parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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\mc{3}{l}{For each parameter set one card V-2}\\
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For each parameter set one card V-2\\
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\hline
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V-2-1 & i3 & multiplicity\\
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V-2-2 & f10.6 & proper dihedral in radians\\
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@ -255,7 +255,7 @@ VI-1-7 & i5 & improper dihedral parameter origin\\
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& & 0: from database, next card ignored \\
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& & 1: from next card\\
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\hline
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\mc{3}{l}{For each parameter set one card VI-2}\\
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For each parameter set one card VI-2\\
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\hline
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VI-2-1 & 3x,f10.6 & improper dihedral in radians\\
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VI-2-2 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$\\
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@ -269,7 +269,7 @@ VI-2-2 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$\\
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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\mc{3}{l}{For each z-matrix definition one card VII}\\
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For each z-matrix definition one card VII\\
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\hline
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VII-1-1 & i5 & atom i \\
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VII-1-2 & i5 & atom j \\
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@ -284,7 +284,7 @@ VII-1-7 & f12.6 & torson i-j-k-l\\
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\end{center}
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\end{table}
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%\section {Format sequence file}
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\section {Format sequence file}
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\begin{table}[h]
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\begin{center}
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@ -326,7 +326,7 @@ II-2-3 & i5 & number of times to repeat cards ($ncount$)\\
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\end{center}
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\end{table}
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%\section {Format trajectory file}
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\section {Format trajectory file}
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\begin{table}[h]
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\begin{center}
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@ -392,8 +392,18 @@ II-4-8 & l1 & logical lps for solute induced dipoles \\
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II-4-5 & i10 & number of solvent molecules \\
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II-4-6 & i10 & number of solvent atoms \\
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II-4-7 & i10 & number of solute atoms \\
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\hline
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\hline
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\hline\hline
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\end{tabular*}
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\caption{Trajectory file format.\label{tbl:nwmdtrj}}
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\end{center}
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\end{table}
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\begin{table}[h]
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\begin{center}
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\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
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\hline\hline
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Card & Format & Description \\ \hline
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\mc{3}{l}{For each solvent molecule one card II-5 for each atom, if stardard precision} \\
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\hline
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II-5-1 & 3f8.3 & solvent atom coordinates, if lxw or lvw \\
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@ -420,11 +430,11 @@ II-6-4 & 3e12.6 & solute atom velocities, if lvs \\
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II-6-7 & 3e12.6 & solute atom forces, if lfs (on new card if both lxs and lvs)\\
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\hline\hline
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\end{tabular*}
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\caption{Trajectory file format.\label{tbl:nwmdtrj}}
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\caption{continued trajectory file format.\label{tbl:nwmdtrj2}}
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\end{center}
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\end{table}
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%\section {Format free energy file}
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\section {Format free energy file}
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\begin{table}[h]
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\begin{center}
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@ -451,7 +461,7 @@ I-4-4 & e20.12 & average exponent forward perturbation energy at current $\lamb
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\end{center}
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\end{table}
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%\section {Format root mean square deviation file}
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\section {Format root mean square deviation file}
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\begin{table}[h]
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\begin{center}
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@ -486,7 +496,7 @@ III-2-3 & f12.6 & average segment rms deviation after superimposition \\
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\end{center}
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\end{table}
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%\section {Format property file}
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\section {Format property file}
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\begin{table}[h]
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\begin{center}
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@ -19,8 +19,8 @@ Search:
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<input type="submit" value="Search">
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</form>
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<P><A HREF="userpdf.pdf">PDF</A>
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<P><A HREF="user.001.ps.Z">Compressed postscript</A> Part 1
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<P><A HREF="user.002.ps.Z">Compressed postscript</A> Part 2
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<P><A HREF="user.001.ps.gz">Compressed postscript</A> Part 1
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<P><A HREF="user.002.ps.gz">Compressed postscript</A> Part 2
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<P><A HREF="user.001.ps">Postscript</A> Part 1
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<P><A HREF="user.002.ps">Postscript</A> Part 2
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<HR>
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