<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2800.1106" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial size=2>
<DIV lang=en
style="PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; PADDING-TOP: 10px"><FONT
size=4>Please, I am trying to calculate an adenine molecule (C5H5N5). I do not
obtain to get resulted. Input could verify this. Thaks.</FONT></DIV>
<DIV lang=en
style="PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; PADDING-TOP: 10px"> </DIV>
<DIV lang=en
style="PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; PADDING-TOP: 10px"><FONT
size=4>Wyllian</FONT></DIV>
<DIV lang=en
style="PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; PADDING-TOP: 10px"><FONT
size=4><A
href="http://www.biophysics.hpg.com.br">http://www.biophysics.hpg.com.br</A>
</FONT> </DIV></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff
size=2>#/bin/sh<BR>####################################################################<BR>#<BR>#
set the needed environment variables<BR>#<BR>.
../../../environment_variables<BR>#<BR># check whether echo needs the -e
option<BR>if [ "`echo -e`" = "-e" ]; then<BR>
echo='echo'<BR>else<BR> echo='echo -e'<BR>fi<BR>#<BR>$echo ' '
<BR>$echo ' running '$0':'<BR>$echo ' pw.x to compute the equilibrium'<BR>$echo
' geometry of a molecule, C5H5N5 - Adenina. '<BR>$echo ' ' <BR>#<BR># check that
needed directories and files exist<BR>#<BR>$echo ' PW_ROOT
is defined as '$PW_ROOT' '<BR>$echo ' PSEUDO_DIR is defined as
'$PSEUDO_DIR' '<BR>$echo ' TMP_DIR is defined as
'$TMP_DIR' '<BR>$echo ' '<BR>$echo ' checking that needed directories and files
exist; \c'<BR>if [ ! -d $PW_ROOT ]; then <BR> $echo;$echo '
STOPPING: directory '$PW_ROOT' does not exist'; exit<BR>else<BR> if [ ! -f
$PW_ROOT/main/pw.x ]; then <BR> echo;echo ' STOPPING:
executable '$PW_ROOT/main/pw.x' does not exist'; exit<BR> fi<BR>fi<BR>if [
! -d $PSEUDO_DIR ]; then <BR> $echo;$echo ' STOPPING: directory
'$PSEUDO_DIR' does not exist'; exit<BR>else<BR> if [ ! -f
$PSEUDO_DIR/H.vbc ]; then <BR> $echo;$echo '
STOPPING: pseudop file '$PSEUDO_DIR/H.vbc' does not exist'; <BR>exit<BR>
fi<BR> if [ ! -f $PSEUDO_DIR/HUS.RRKJ3 ]; then
<BR> $echo;$echo ' STOPPING: pseudop file
'$PSEUDO_DIR/HUS.RRKJ3' does not exis<BR>t'; exit<BR> fi<BR> if [ !
-f $PSEUDO_DIR/HUSPBE.RRKJ3 ]; then<BR>
$echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUSPBE.RRKJ3' does not
e<BR>xist'; exit<BR> fi<BR> if [ ! -f $PSEUDO_DIR/C.vbc ];
then<BR> $echo;$echo ' STOPPING: pseudop file
'$PSEUDO_DIR/C.vbc' does not exist'; <BR>exit<BR> fi<BR> if [ ! -f
$PSEUDO_DIR/CUS.RRKJ3 ]; then<BR> $echo;$echo '
STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not exist'; <BR>exit<BR>
fi<BR> if [ ! -f $PSEUDO_DIR/CUSPBE.RRKJ3 ];
then<BR> $echo;$echo ' STOPPING: pseudop file
'$PSEUDO_DIR/CUSPBE.RRKJ3' does not e<BR>xist'; exit<BR> fi<BR> if [
! -f $PSEUDO_DIR/NUSPBE.RRKJ3 ]; then<BR>
$echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUSPBE.RRKJ3' does not
e<BR>xist'; exit<BR> fi<BR> if [ ! -f $PSEUDO_DIR/NUS.RRKJ3 ];
then<BR> $echo;$echo ' STOPPING: pseudop file
'$PSEUDO_DIR/NUS.RRKJ3' does not exis<BR>t'; exit<BR> fi<BR>fi<BR>if
[ i! -d $TMP_DIR ]; then <BR> $echo;$echo ' STOPPING:
directory '$TMP_DIR' does not exist'; exit<BR>fi</FONT></DIV>
<DIV><FONT color=#0000ff></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>$echo ' done'<BR>#<BR># clean
TMP_DIR<BR>#<BR> $echo ' cleaning '$TMP_DIR' ; \c'<BR>rm -f
$TMP_DIR/*<BR>$echo ' done'<BR>#<BR># self-consistent calculation<BR>#<BR>cat
> adenina1.in << EOF<BR>C5H5N5 molecule +
relax<BR>C5H5N5<BR> &input<BR> ibrav=0,
celldm(1)=1.d0, nat=15,ntyp=3,<BR> pseudop(1) =
'CUS.RRKJ3', <BR> pseudop(2) =
'HUS.RRKJ3',<BR> pseudop(3) =
'NUS.RRKJ3',<BR> pseudo_dir = '$PSEUDO_DIR/',
<BR> tmp_dir='$TMP_DIR/',<BR> ecut(1)=24.0,
dual=6,<BR> beta(1)=0.3, upscale=10,<BR> tr2
= 1.0d-14, iswitch=1,<BR> niter=100,
nstep=100,<BR>
output_pot='c5h5n5pot',<BR> &end<BR>14.0 0.0
0.0<BR> 0.0 14.0 0.0<BR> 0.0 0.0
14.0<BR>cubic<BR>-4.279664 -2.380489 0.676900 1<BR> 0.015307
-2.366316 0.844708 1<BR> 0.010016 0.051590 -0.222799
1<BR>-2.329655 1.250432 -0.851322 1<BR> 3.897562 -0.881558
0.346576 1<BR>-6.079629 -3.364659 1.041240 2<BR> 3.257511
-4.583532 1.953033 2<BR> 5.965679 -8.416466 0.418008
2<BR>-0.491329 4.467314 -2.209657 2<BR>-3.950852 4.517203 -2.374064
2<BR> 2.453432 0.933336 -0.511738 3<BR>-2.252932 3.610512
-1.899176 3<BR> 2.527699 -2.915659 1.188827 3<BR>-2.199264
-3.629598 1.310904 3<BR>-4.478275 -0.033070 -0.369631 3<BR>'C ' 1 1
1.0<BR>'H ' 1 2 1.0<BR>'N ' 1 3 1.0 <BR> 0<BR> 1 1 1<BR> 0
0 0 <BR>EOF<BR>$echo ' running the geometry relaxation for adenina;
\c'<BR>$PARA_PREFIX $PW_ROOT/main/pw.x $PARA_POSTFIX < adenina1.in >
adenina1.out<BR>$echo ' Adenina done'<BR></DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR>---<BR>Outgoing mail is certified Virus Free.<BR>Checked by AVG
anti-virus system (<A
href="http://www.grisoft.com">http://www.grisoft.com</A>).<BR>Version: 6.0.481 /
Virus Database: 277 - Release Date: 13/5/2003</FONT></DIV></BODY></HTML>