[Pw_forum] I am with problems to calculate a molecule: adenine (C5H5N5)

[Wyllian]

Please, I am trying to calculate an adenine molecule (C5H5N5). I do not obtain to get resulted. Input could verify this. Thaks.

Wyllian
http://www.biophysics.hpg.com.br  



#/bin/sh
####################################################################
#
# set the needed environment variables
#
. ../../../environment_variables
#
# check whether echo needs the -e option
if [ "`echo -e`" = "-e" ]; then
   echo='echo'
else
   echo='echo -e'
fi
#
$echo ' ' 
$echo ' running '$0':'
$echo ' pw.x to compute the equilibrium'
$echo ' geometry of a molecule, C5H5N5 - Adenina. '
$echo ' ' 
#
# check that needed directories and files exist
#
$echo ' PW_ROOT    is  defined as '$PW_ROOT' '
$echo ' PSEUDO_DIR is  defined as '$PSEUDO_DIR' '
$echo ' TMP_DIR    is  defined as '$TMP_DIR' '
$echo ' '
$echo ' checking that needed directories and files exist; \c'
if [ ! -d $PW_ROOT ]; then 
   $echo;$echo ' STOPPING: directory '$PW_ROOT' does not exist'; exit
else
  if [ ! -f $PW_ROOT/main/pw.x ]; then 
     echo;echo ' STOPPING: executable '$PW_ROOT/main/pw.x' does not exist'; exit
  fi
fi
if [ ! -d $PSEUDO_DIR ]; then 
   $echo;$echo ' STOPPING: directory '$PSEUDO_DIR' does not exist'; exit
else
  if [ ! -f $PSEUDO_DIR/H.vbc ]; then 
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/H.vbc' does not exist'; 
exit
  fi
  if [ ! -f $PSEUDO_DIR/HUS.RRKJ3 ]; then 
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUS.RRKJ3' does not exis
t'; exit
  fi
  if [ ! -f $PSEUDO_DIR/HUSPBE.RRKJ3 ]; then
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/HUSPBE.RRKJ3' does not e
xist'; exit
  fi
  if [ ! -f $PSEUDO_DIR/C.vbc ]; then
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not exist'; 
exit
  fi
  if [ ! -f $PSEUDO_DIR/CUS.RRKJ3 ]; then
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/C.vbc' does not exist'; 
exit
  fi
  if [ ! -f $PSEUDO_DIR/CUSPBE.RRKJ3 ]; then
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/CUSPBE.RRKJ3' does not e
xist'; exit
  fi
  if [ ! -f $PSEUDO_DIR/NUSPBE.RRKJ3 ]; then
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUSPBE.RRKJ3' does not e
xist'; exit
  fi
  if [ ! -f $PSEUDO_DIR/NUS.RRKJ3 ]; then
      $echo;$echo ' STOPPING: pseudop file '$PSEUDO_DIR/NUS.RRKJ3' does not exis
t'; exit
  fi
fi
if [   i! -d $TMP_DIR ]; then 
   $echo;$echo ' STOPPING: directory '$TMP_DIR' does not exist'; exit
fi

$echo ' done'
#
# clean TMP_DIR
#
 $echo ' cleaning '$TMP_DIR' ; \c'
rm -f $TMP_DIR/*
$echo ' done'
#
# self-consistent calculation
#
cat > adenina1.in << EOF
C5H5N5 molecule + relax
C5H5N5
 &input
    ibrav=0, celldm(1)=1.d0, nat=15,ntyp=3,
    pseudop(1) = 'CUS.RRKJ3',  
    pseudop(2) = 'HUS.RRKJ3',
    pseudop(3) = 'NUS.RRKJ3',
    pseudo_dir =  '$PSEUDO_DIR/', 
    tmp_dir='$TMP_DIR/',
    ecut(1)=24.0, dual=6,
    beta(1)=0.3, upscale=10,
    tr2 = 1.0d-14, iswitch=1,
    niter=100, nstep=100,
    output_pot='c5h5n5pot',
 &end
14.0   0.0   0.0
 0.0  14.0   0.0
 0.0   0.0  14.0
cubic
-4.279664 -2.380489  0.676900 1
 0.015307 -2.366316  0.844708 1
 0.010016  0.051590 -0.222799 1
-2.329655  1.250432 -0.851322 1
 3.897562 -0.881558  0.346576 1
-6.079629 -3.364659  1.041240 2
 3.257511 -4.583532  1.953033 2
 5.965679 -8.416466  0.418008 2
-0.491329  4.467314 -2.209657 2
-3.950852  4.517203 -2.374064 2
 2.453432  0.933336 -0.511738 3
-2.252932  3.610512 -1.899176 3
 2.527699 -2.915659  1.188827 3
-2.199264 -3.629598  1.310904 3
-4.478275 -0.033070 -0.369631 3
'C ' 1 1 1.0
'H ' 1 2 1.0
'N ' 1 3 1.0  
 0
 1 1 1
 0 0 0 
EOF
$echo ' running the geometry relaxation for adenina; \c'
$PARA_PREFIX $PW_ROOT/main/pw.x $PARA_POSTFIX < adenina1.in > adenina1.out
$echo ' Adenina done'




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