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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Hi, I’m trying to use g_velacc to
compute the velocity autocorrelation function for a set of molecules.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>When I compute g_velacc for atoms it gives
the correct answer (I wrote my own program to check)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>When I compute it for molecules (with
option –mol and and index file with molecules not atoms)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>I get strange results.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>I looked at the source code (admitedly I’m
a much better fortran programmer than c) but these few lines look weird to me.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Can anybody tell me if <span
style='mso-spacerun:yes'> </span>line 7 to 9 they are right or not?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span>1<span
style='mso-spacerun:yes'> </span>if (bMol)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span><span
style='mso-spacerun:yes'> </span>2<span
style='mso-spacerun:yes'> </span>for(i=0; i<gnx;
i++) {<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span style='mso-spacerun:yes'>
</span><span style='mso-spacerun:yes'> </span>3<span
style='mso-spacerun:yes'>
</span>clear_rvec(mv_mol);<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span style='mso-spacerun:yes'>
</span><span style='mso-spacerun:yes'> </span>4<span
style='mso-spacerun:yes'> </span>for(j=0;
j<atndx[index[i]+1] - atndx[index[i]]; j++) {<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span>5<span
style='mso-spacerun:yes'> </span>at =
a[atndx[index[i]]+j];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span>6<span
style='mso-spacerun:yes'> </span>m<span
style='mso-spacerun:yes'> </span>= top.atoms.atom[at].m;<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span style='mso-spacerun:yes'>
</span><span style='mso-spacerun:yes'> </span>7 <span
style='mso-spacerun:yes'> </span>mv_mol[XX] += m*fr.v[at][XX];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span>8 <span
style='mso-spacerun:yes'> </span>mv_mol[XX] += m*fr.v[at][YY];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span style='mso-spacerun:yes'>
</span><span style='mso-spacerun:yes'> </span>9<span
style='mso-spacerun:yes'> </span>mv_mol[XX] += m*fr.v[at][ZZ];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span>}<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'>
</span>c1[i][tel3+XX]=mv_mol[XX];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'>
</span>c1[i][tel3+YY]=mv_mol[YY];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'>
</span>c1[i][tel3+ZZ]=mv_mol[ZZ];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span>}<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>shouldn’t it be <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'>
</span>mv_mol[XX] += m*fr.v[at][XX];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'> </span><span
style='mso-spacerun:yes'> </span>mv_mol[YY] += m*fr.v[at][YY];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style='mso-spacerun:yes'>
</span>mv_mol[ZZ] += m*fr.v[at][ZZ];<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>if this is computing the velocity of center
of mass of the molecule?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Thanks!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Claudio.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><o:p> </o:p></span></font></p>
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