[Pw_forum] Fwd: Re: parameteres of quantum dots
pablohi
pablohi at correo.ugr.es
Sat Nov 22 21:32:44 CET 2014
Thank you very much for your answer, this is the entire script. I
suppose I have to check with a few simulations
#!/bin/bash
#$ -S /bin/bash
#$ -q NOParalela
#$ -l NOParalela
#$ -o QE03.out
#$ -e QEerror03.out
# module load alhambra/espresso-5.0.2
# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
# run from directory where this script is
# cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
# set the needed environment variables
#. ../../../environment_variables
# required executables and pseudopotentials
PARA_PREFIX=""
PARA_POSTFIX=" -nband 1 -ntg 1 "
PREFIX="/usr/local/apps/espresso-5.0.2"
BIN_DIR=$PREFIX/bin
PSEUDO_DIR=/usr/local/admin/home/TIC105/trinidadgcia/pseudo
NETWORK_PSEUDO=http://www.quantum-espresso.org/wp-content/uploads/upf_files/
EXAMPLE_DIR=/usr/local/admin/home/TIC105/trinidadgcia/SCRACTH
RESULTS_DIR=$EXAMPLE_DIR/results03
TMP_DIR=$EXAMPLE_DIR/tmp03
BIN_LIST="pw.x"
PSEUDO_LIST="H.pbe-van_bm.UPF Ni.pbe-nd-rrkjus.UPF Fe.pz-nd-rrkjus.UPF
\
O.pbe-rrkjus.UPF Se.pbe-van.UPF Cd.pbe-n-van.UPF"
# check for directories
for DIR in "$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" "$RESULTS_DIR" ; do
if test ! -d $DIR ; then
mkdir $DIR
fi
done
# 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
cd $RESULTS_DIR
$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"
$ECHO
$ECHO "$RESULTS_DIR : starting"
$ECHO
$ECHO "Script para calcular el espectro de energías de puntos cuánticos
de CdSe."
$ECHO "Primero se realizará un cálculo autoconsistente"
$ECHO "para calcular el espectro de CdSe."
# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation
cat > CdSe.scf.in << EOF
CdSe
Cadmium Selenide
&control
calculation='scf'
restart_mode='from_scratch',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
prefix='CdSe'
/
&system
ibrav = 0, nat= 79, ntyp= 3,
ecutwfc = 10.0,ecutrho = 80.0,
report=1,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05
noncolin = .false.
/
&electrons
conv_thr = 1.0e-8
mixing_beta = 0.2
/
CELL_PARAMETERS {bohr}
32.5033024000 0.0000000000 0.0000000000
-16.2516512000 28.1486855853 0.0000000000
0.0000000000 0.0000000000 39.8082529177
ATOMIC_SPECIES
Se 78.960 Se.pbe-van.UPF
Cd 112.411 Cd.pbe-n-van.UPF
H 1.00794 H.pbe-van_bm.UPF
ATOMIC_POSITIONS {bohr}
Cd 0.3333333 0.1666667 0.5520833
Cd 0.2500000 0.2500000 0.3854167
Cd 0.3333333 0.4166667 0.5520833
Cd 0.5000000 0.2500000 0.3854167
Cd 0.5833333 0.4166667 0.5520833
Cd 0.2500000 0.5000000 0.3854167
Cd 0.3333333 0.6666667 0.5520833
Cd 0.5000000 0.5000000 0.3854167
Cd 0.5833333 0.6666667 0.5520833
Cd 0.7500000 0.5000000 0.3854167
Cd 0.8333333 0.6666667 0.5520833
Cd 0.5000000 0.7500000 0.3854167
Cd 0.7500000 0.7500000 0.3854167
Cd 0.2500000 0.2500000 0.7187500
Cd 0.5000000 0.2500000 0.7187500
Cd 0.2500000 0.5000000 0.7187500
Cd 0.5000000 0.5000000 0.7187500
Cd 0.7500000 0.5000000 0.7187500
Cd 0.5000000 0.7500000 0.7187500
Cd 0.7500000 0.7500000 0.7187500
Se 0.3333333 0.1666667 0.3437500
Se 0.3333333 0.4166667 0.3437500
Se 0.5833333 0.4166667 0.3437500
Se 0.3333333 0.6666667 0.3437500
Se 0.5833333 0.6666667 0.3437500
Se 0.8333333 0.6666667 0.3437500
Se 0.3333333 0.1666667 0.6770833
Se 0.2500000 0.2500000 0.5104167
Se 0.3333333 0.4166667 0.6770833
Se 0.5000000 0.2500000 0.5104167
Se 0.5833333 0.4166667 0.6770833
Se 0.2500000 0.5000000 0.5104167
Se 0.3333333 0.6666667 0.6770833
Se 0.5000000 0.5000000 0.5104167
Se 0.5833333 0.6666667 0.6770833
Se 0.7500000 0.5000000 0.5104167
Se 0.8333333 0.6666667 0.6770833
Se 0.5000000 0.7500000 0.5104167
Se 0.7500000 0.7500000 0.5104167
H 0.2875000 0.0750000 0.5291667
H 0.1583333 0.2041667 0.3625000
H 0.5458333 0.2041667 0.3625000
H 0.1583333 0.4541667 0.3625000
H 0.2875000 0.7125000 0.5291667
H 0.7958333 0.4541667 0.3625000
H 0.9250000 0.7125000 0.5291667
H 0.5458333 0.8416667 0.3625000
H 0.7958333 0.8416667 0.3625000
H 0.1583333 0.2041667 0.6958333
H 0.2500000 0.2500000 0.7875000
H 0.5458333 0.2041667 0.6958333
H 0.5000000 0.2500000 0.7875000
H 0.1583333 0.4541667 0.6958333
H 0.2500000 0.5000000 0.7875000
H 0.5000000 0.5000000 0.7875000
H 0.7958333 0.4541667 0.6958333
H 0.7500000 0.5000000 0.7875000
H 0.5458333 0.8416667 0.6958333
H 0.5000000 0.7500000 0.7875000
H 0.7958333 0.8416667 0.6958333
H 0.7500000 0.7500000 0.7875000
H 0.3333333 0.1666667 0.3062500
H 0.3083333 0.1166667 0.3562500
H 0.3333333 0.4166667 0.3125000
H 0.5833333 0.4166667 0.3125000
H 0.3333333 0.6666667 0.3062500
H 0.3083333 0.6916667 0.3562500
H 0.5833333 0.6666667 0.3125000
H 0.8333333 0.6666667 0.3062500
H 0.8833333 0.6916667 0.3562500
H 0.3125000 0.1250000 0.6875000
H 0.2083333 0.2291667 0.5208333
H 0.5208333 0.2291667 0.5208333
H 0.2083333 0.4791667 0.5208333
H 0.3125000 0.6875000 0.6875000
H 0.7708333 0.4791667 0.5208333
H 0.8750000 0.6875000 0.6875000
H 0.5208333 0.7916667 0.5208333
H 0.7708333 0.7916667 0.5208333
K_POINTS {gamma}
EOF
$ECHO " running the scf calculation for CdSe...\c"
$PW_COMMAND < CdSe.scf.in > CdSe.scf.out
check_failure $?
$ECHO " done"
# band structure calculation
cat > CdSe.band.in << EOF
CdSe
Cadmium Selenide
&control
calculation='bands'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
prefix='CdSe'
/
&system
ibrav = 0, nat= 79, ntyp= 3,
ecutwfc = 10.0,ecutrho = 80.0,
report=1, nbnd = 16
noncolin = .false.
/
&electrons
conv_thr = 1.0e-8
mixing_beta = 0.2
/
CELL_PARAMETERS {bohr}
32.5033024000 0.0000000000 0.0000000000
-16.2516512000 28.1486855853 0.0000000000
0.0000000000 0.0000000000 39.8082529177
ATOMIC_SPECIES
Se 78.960 Se.pbe-van.UPF
Cd 112.411 Cd.pbe-n-van.UPF
H 1.00794 H.pbe-van_bm.UPF
ATOMIC_POSITIONS {bohr}
Cd 0.3333333 0.1666667 0.5520833
Cd 0.2500000 0.2500000 0.3854167
Cd 0.3333333 0.4166667 0.5520833
Cd 0.5000000 0.2500000 0.3854167
Cd 0.5833333 0.4166667 0.5520833
Cd 0.2500000 0.5000000 0.3854167
Cd 0.3333333 0.6666667 0.5520833
Cd 0.5000000 0.5000000 0.3854167
Cd 0.5833333 0.6666667 0.5520833
Cd 0.7500000 0.5000000 0.3854167
Cd 0.8333333 0.6666667 0.5520833
Cd 0.5000000 0.7500000 0.3854167
Cd 0.7500000 0.7500000 0.3854167
Cd 0.2500000 0.2500000 0.7187500
Cd 0.5000000 0.2500000 0.7187500
Cd 0.2500000 0.5000000 0.7187500
Cd 0.5000000 0.5000000 0.7187500
Cd 0.7500000 0.5000000 0.7187500
Cd 0.5000000 0.7500000 0.7187500
Cd 0.7500000 0.7500000 0.7187500
Se 0.3333333 0.1666667 0.3437500
Se 0.3333333 0.4166667 0.3437500
Se 0.5833333 0.4166667 0.3437500
Se 0.3333333 0.6666667 0.3437500
Se 0.5833333 0.6666667 0.3437500
Se 0.8333333 0.6666667 0.3437500
Se 0.3333333 0.1666667 0.6770833
Se 0.2500000 0.2500000 0.5104167
Se 0.3333333 0.4166667 0.6770833
Se 0.5000000 0.2500000 0.5104167
Se 0.5833333 0.4166667 0.6770833
Se 0.2500000 0.5000000 0.5104167
Se 0.3333333 0.6666667 0.6770833
Se 0.5000000 0.5000000 0.5104167
Se 0.5833333 0.6666667 0.6770833
Se 0.7500000 0.5000000 0.5104167
Se 0.8333333 0.6666667 0.6770833
Se 0.5000000 0.7500000 0.5104167
Se 0.7500000 0.7500000 0.5104167
H 0.2875000 0.0750000 0.5291667
H 0.1583333 0.2041667 0.3625000
H 0.5458333 0.2041667 0.3625000
H 0.1583333 0.4541667 0.3625000
H 0.2875000 0.7125000 0.5291667
H 0.7958333 0.4541667 0.3625000
H 0.9250000 0.7125000 0.5291667
H 0.5458333 0.8416667 0.3625000
H 0.7958333 0.8416667 0.3625000
H 0.1583333 0.2041667 0.6958333
H 0.2500000 0.2500000 0.7875000
H 0.5458333 0.2041667 0.6958333
H 0.5000000 0.2500000 0.7875000
H 0.1583333 0.4541667 0.6958333
H 0.2500000 0.5000000 0.7875000
H 0.5000000 0.5000000 0.7875000
H 0.7958333 0.4541667 0.6958333
H 0.7500000 0.5000000 0.7875000
H 0.5458333 0.8416667 0.6958333
H 0.5000000 0.7500000 0.7875000
H 0.7958333 0.8416667 0.6958333
H 0.7500000 0.7500000 0.7875000
H 0.3333333 0.1666667 0.3062500
H 0.3083333 0.1166667 0.3562500
H 0.3333333 0.4166667 0.3125000
H 0.5833333 0.4166667 0.3125000
H 0.3333333 0.6666667 0.3062500
H 0.3083333 0.6916667 0.3562500
H 0.5833333 0.6666667 0.3125000
H 0.8333333 0.6666667 0.3062500
H 0.8833333 0.6916667 0.3562500
H 0.3125000 0.1250000 0.6875000
H 0.2083333 0.2291667 0.5208333
H 0.5208333 0.2291667 0.5208333
H 0.2083333 0.4791667 0.5208333
H 0.3125000 0.6875000 0.6875000
H 0.7708333 0.4791667 0.5208333
H 0.8750000 0.6875000 0.6875000
H 0.5208333 0.7916667 0.5208333
H 0.7708333 0.7916667 0.5208333
K_POINTS {gamma}
EOF
$ECHO " running the energies spectrum for CdSe...\c"
$PW_COMMAND < CdSe.band.in > CdSe.band.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
Pablo Hidalgo Romera
Electronics and computer architecture department(Student)
University of Granada
Spain
-------- Mensaje original --------
Asunto: Re: [Pw_forum] parameteres of quantum dots
Fecha: 2014-11-22 18:40
Remitente: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
Destinatario: pw_forum at pwscf.org
Respuesta a: PWSCF Forum <pw_forum at pwscf.org>
Dear Pablo
Who knows?
Your input seems very strange to me, but it is very difficult to
evaluate from such a little scrap...
Please, remember to sign always your posts to this forum with your
scientific affiliation.
HTH
Giuseppe
Giuseppe Mattioli
ISM-CNR
Italy
Quoting pablohi <pablohi at correo.ugr.es>:
> Dear Quantum Espresso
>
> I want to simulate the energies spectrum of CdSe Quantum Dots, and I
> have used the following parameters system parameters:
>
> &system
> ibrav = 0, nat= 79, ntyp= 3,
> ecutwfc = 25.0,ecutrho = 100.0,
> report=1,
> occupations='smearing', smearing='marzari-vanderbilt',
> degauss=0.05
> noncolin = .true.
> starting_magnetization(1) = 0.5
> angle1(1) = 90.0
> angle2(1) = 0.0
>
> I need to know if there are other parameters that are more
> appropiate.
>
> Thanks in advance
>
> Pablo Hidalgo Romera
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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