[QE-users] Energy of isolated atom of CaO

[Pietro Delugas]

The Ca pseudo that you are using has 2 electrons in  valence 4s plus  semicore electrons in  3s and 3p, with your occupation you have to allocate 10 electrons, your input occupation should be something like 
2.0  2.0  2.0  2.0  2.0  



Sent from Mail for Windows 10

From: Pooja Vyas
Sent: Friday, June 26, 2020 8:40 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Energy of isolated atom of CaO

I also tried to compute separate isolated energies for Ca and O (example05/PW). For Ca, I used the following script, But I face an error "strange occupations: number of electrons from occupations is wrong."

#!/bin/sh

# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=`pwd`

# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi

$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to calculate the total energy of an isolated"
$ECHO "atom in a supercell with fixed occupations."
$ECHO "Energy of Ca"

# set the needed environment variables
. ../../../environment_variables

# required executables and pseudopotentials
BIN_LIST="pw.x"
PSEUDO_LIST=" Ca.pbe-nsp-van.UPF"

$ECHO
$ECHO "  executables directory: $BIN_DIR"
$ECHO "  pseudo directory:      $PSEUDO_DIR"
$ECHO "  temporary directory:   $TMP_DIR"
$ECHO "  checking that needed directories and files exist...\c"

# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
    if test ! -d $DIR ; then
        $ECHO
        $ECHO "ERROR: $DIR not existent or not a directory"
        $ECHO "Aborting"
        exit 1
    fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
    if test ! -d $DIR ; then
        mkdir $DIR
    fi
done
cd $EXAMPLE_DIR/results

# check for executables
for FILE in $BIN_LIST ; do
    if test ! -x $BIN_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
        $ECHO "Aborting"
        exit 1
    fi
done

# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
    if test ! -r $PSEUDO_DIR/$FILE ; then
       $ECHO
       $ECHO "Downloading $FILE to $PSEUDO_DIR...\c"
            $WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null
    fi
    if test $? != 0; then
        $ECHO
        $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
        $ECHO "Aborting"
        exit 1
    fi
done
$ECHO " done"

# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
$ECHO
$ECHO "  running pw.x as: $PW_COMMAND"
$ECHO

# self-consistent calculation for isolated Ca atom
cat > Ca.in << EOF
 &control
    calculation='scf',
    restart_mode='from_scratch',
    pseudo_dir='$PSEUDO_DIR/'
    outdir='$TMP_DIR/'
 /
 &system
   ibrav=1,
   celldm(1)=24.0,
   nat=1,
   ntyp=1,
   nbnd=12,
   nosym=.true.,
   ecutwfc=100.0,
   occupations='from_input',
 /
 &electrons
   mixing_beta=0.7,
   conv_thr=1.0E-8,
 /
ATOMIC_SPECIES
Ca     40.078    Ca.pbe-nsp-van.UPF
ATOMIC_POSITIONS
Ca      0.0   0.0     0.0
K_POINTS  Gamma

OCCUPATIONS
2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
EOF
$ECHO "  running self-consistent calculation for Al atom...\c"
$PW_COMMAND < Ca.in > Ca.out
check_failure $?
$ECHO " done"



# clean TMP_DIR
$ECHO "  cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"


$ECHO
$ECHO "$EXAMPLE_DIR: done"

Can anyone suggest how should the occupation number be written in above case?
Thanks and regards.

On Fri, Jun 26, 2020 at 11:58 AM Pietro Delugas <pdelugas at sissa.it> wrote:
Hello 
 
In ATOMIC_POSITIONS  you need to specify the units that you are  using for the coordinates, if you don’t put anything he program assumes alat units and puts the 2 atoms very far apart. 
 
If you actually wanted  compute the two separated atoms specifying startingwfc=’random’ in the &electrons name list may help.  In this case I would also chose calculation=’scf’ in &control. 
 
Regards - Pietro  
 
Sent from Mail for Windows 10
 
From: Pooja Vyas
Sent: Friday, June 26, 2020 8:12 AM
To: Quantum ESPRESSO users Forum
Subject: [QE-users] Energy of isolated atom of CaO
 
Dear users,
I want to calculate cohesive energy of CaO. I'm using cluster_example/PW which uses assume_isolated = 'martyna_tuckerman' . Following is my input script:
 
#!/bin/sh
for a in 30
do
cat > ${a}.in << EOF
&CONTROL
  calculation  = 'relax'
  prefix       = "${a}",
  pseudo_dir   = "/home/user/pv/cohesive/pseudo/",
  outdir       = "/home/user/pv/cohesive/",
/
&SYSTEM
  ibrav     = 1,
  celldm(1) = $a,
  nat       = 2,
  ntyp      = 2,
  ecutwfc   = 100.D0,
  assume_isolated = 'martyna-tuckerman'
/
&ELECTRONS
  conv_thr    = 1.D-8,
  mixing_beta = 0.7D0,
/
&IONS
/
ATOMIC_SPECIES
Ca  40.078  Ca.pbe-nsp-van.UPF
O  15.999  O.pbe-van_ak.UPF
ATOMIC_POSITIONS 
Ca 0.0 0.0 0.0
O  0.5 0.5 0.5
K_POINTS Gamma

EOF

mpirun -np 40 -machinefile x1 /apps/codes/qe/6.4/bin/pw.x < ${a}.in > ${a}.out
done
done
 
My lattice constant is around 8 a.u , so I assumed the box size to be 3 times of it. But when I run the script, the convergence was not achieved even after 100 iterations. Then I tried to take small box size of about 16 bohr. That too didn't work. Then I even tried reducing ecutwfc and mixing_beta..but same error was obtained. Can anyone suggest what can I do to resolve the issue?
Any kind of help is appreciated.
Thanks and regards.
 
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