[Pw_forum] problem in phonon DOS calculation of HCP structure (Job details)

Wed Sep 14 16:25:07 CEST 2005

Dear all, 

The following are the input files in my calculations.

Thanks a lot!

Sincerely,

Yi Kong

**************** to get the dynamical matrix *************

# how to run execubles
PW_COMMAND="mpirun -np 8 $BIN_DIR/pw.x -npool 4"
PH_COMMAND="mpirun -np 8 $BIN_DIR/ph.x -npool 4"
$ECHO
$ECHO "  running pw.x as:     $PW_COMMAND"
$ECHO "  running ph.x as:     $PH_COMMAND"
$ECHO

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

# self-consistent calculation
cat > PdRu3.scf.in <http://PdRu3.scf.in> << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    tprnfor= .true.
    prefix='PdRu3',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system    
    ibrav=  4, celldm(1) = 10.44, celldm(3)= 0.793 , nat=  8, ntyp= 2,
    ecutwfc =30.0, ecutrho = 300.0,
    occupations='smearing',degauss=0.02,
    smearing='marzari-vanderbilt'
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.3
    mixing_mode = 'plain'
    diagonalization='david'
    mixing_ndim=8
 /
ATOMIC_SPECIES
 Ru 101.07 Ru.pbe-n-van.UPF
 Pd 106.4  Pd.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
 Ru 0.50       0.0       0.00 0 0 0 
 Ru 0.50       0.50      0.00 0 0 0 
 Ru 0.00       0.50      0.00 0 0 0
 Ru 0.333333   0.1666667 0.50 0 0 0 
 Ru 0.833333   0.1666667 0.50 0 0 0 
 Ru 0.833333   0.6666667 0.50 0 0 0
 Pd 0.00       0.00      0.00 0 0 0
 Pd 0.333333   0.6666667 0.50 0 0 0
K_POINTS AUTOMATIC
 8 8 8 0 0 0 
EOF
$ECHO "  running the scf calculation...\c"
$PW_COMMAND < PdRu3.scf.in <http://PdRu3.scf.in> > PdRu3.scf.out
$ECHO " done"

# phonons
cat > PdRu3.phG.in <http://PdRu3.phG.in> << EOF
phonons of PdRu3 at Gamma
 &inputph
  tr2_ph=1.0d-12,
  prefix='PdRu3',
  amass(2)=106.4,
  amass(1)=101.07,
  outdir='$TMP_DIR/',
  fildyn='PdRu3.dynG',
 /0.0 0.0 0.0
EOF
$ECHO "  running the phonon calculation at Gamma...\c"
$PH_COMMAND < PdRu3.phG.in <http://PdRu3.phG.in> > PdRu3.phG.out
$ECHO " done"

# These are k-points of a (444) uniform grid in the irreducible
# Brillouin Zone of the bcc lattice (Gamma is treated separately)
/bin/rm PdRu3.nscf.out PdRu3.ph.out

qpoints="0.0000000,0.0000000,0.3152585\
         0.0000000,0.0000000,-0.6305170\
         0.0000000,0.2886751,0.0000000\
         0.0000000,0.2886751,0.3152585\
         0.0000000,0.2886751,-0.6305170\
         0.0000000,-0.5773503,0.0000000\
         0.0000000,-0.5773503,0.3152585\
         0.0000000,-0.5773503,-0.6305170\
         0.2500000,0.4330127,0.0000000\
         0.2500000,0.4330127,0.3152585\
         0.2500000,0.4330127,-0.6305170"

for qpoint in $qpoints ; do

# non self-consistent calculation 
qx=`$ECHO $qpoint | cut -d, -f1`
qy=`$ECHO $qpoint | cut -d, -f2`
qz=`$ECHO $qpoint | cut -d, -f3`
cat > PdRu3.nscf.in <http://PdRu3.nscf.in> << EOF
 &control
    calculation='phonon'
    restart_mode='from_scratch',
    prefix='PdRu3',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system    
    ibrav=  4, celldm(1) = 10.44, celldm(3)= 0.793 , nat=  8, ntyp= 2,
    ecutwfc =30.0, ecutrho = 300.0,
    occupations='smearing',degauss=0.02,
    smearing='marzari-vanderbilt'
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.3
    mixing_mode = 'plain'
    diagonalization='david'
    mixing_ndim=8
 /
 &phonon
    xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz
 /
ATOMIC_SPECIES
 Ru 101.07 Ru.pbe-n-van.UPF
 Pd 106.4  Pd.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
 Ru 0.50       0.0       0.00 0 0 0 
 Ru 0.50       0.50      0.00 0 0 0 
 Ru 0.00       0.50      0.00 0 0 0
 Ru 0.333333   0.1666667 0.50 0 0 0 
 Ru 0.833333   0.1666667 0.50 0 0 0 
 Ru 0.833333   0.6666667 0.50 0 0 0
 Pd 0.00       0.00      0.00 0 0 0
 Pd 0.333333   0.6666667 0.50 0 0 0
K_POINTS AUTOMATIC
 8 8 8 0 0 0
EOF

$ECHO "  running the nscf calculation at q=$qpoint...\c"
$PW_COMMAND < PdRu3.nscf.in <http://PdRu3.nscf.in> >> PdRu3.nscf.out
$ECHO " done"

# phonon calculation
cat > PdRu3.ph.in <http://PdRu3.ph.in> << EOF
phonons of PdRu3 at $qpoint
 &inputph
  tr2_ph=1.0d-12,
  prefix='PdRu3',
  amass(2)=106.4,
  amass(1)=101.07,
  outdir='$TMP_DIR/',
  fildyn='dyn.$qpoint'
  alpha_mix(1)=0.3
 /
$qpoint
EOF
$ECHO "  running the phonon calculation at q=$qpoint...\c"
$PH_COMMAND < PdRu3.ph.in <http://PdRu3.ph.in> >> PdRu3.ph.out
$ECHO " done"

done

$ECHO
$ECHO "$CURRENT_DIR: done"

******************** to get the force constants ********
# how to run execubles
Q2R_COMMAND="mpirun -np 8 $BIN_DIR/q2r.x "
$ECHO
$ECHO "  running q2r.x as:    $Q2R_COMMAND" 
$ECHO

cat > q2r.in <http://q2r.in> << EOF
&input
  nr1=4, nr2=4, nr3=4, fild='pd3ru444.fc'
/
12 pd3ru.dynGdyn.0.0000000,0.0000000,0.3152585dyn.0.0000000,0.0000000,-0.6305170dyn.0.0000000,0.2886751,0.0000000dyn.0.0000000,0.2886751,0.3152585dyn.0.0000000,0.2886751,-0.6305170dyn.0.0000000,-0.5773503,0.0000000dyn.0.0000000,-0.5773503,0.3152585dyn.0.0000000,-0.5773503,-0.6305170dyn.0.2500000,0.4330127,0.0000000dyn.0.2500000,0.4330127,0.3152585dyn.0.2500000,0.4330127,-0.6305170
EOF

$ECHO "transforming C(q)=>C(R)...\c"
$Q2R_COMMAND < q2r.in <http://q2r.in> > q2r.out
$ECHO "done"

$ECHO
$ECHO "$CURRENT_DIR: done"

***************** to get the phonon DOS *********
# how to run execubles
MATDYN_COMMAND="$PARA_PREFIX $BIN_DIR/matdyn.x $PARA_POSTFIX"
$ECHO
$ECHO "  running matdyn.x as: $MATDYN_COMMAND"
$ECHO
cat >phdos.in <http://phdos.in> <<EOF
&input
  asr=.true., dos =.true., amass(2)=106.4,amass(1)=101.07,
  flfrc='Pd3Ru444.fc',fldos='Pd3Ru.phdos',nk1=20,nk2=20,nk3=20
/
EOF

$ECHO " calculating phonon DOS...\c"
$MATDYN_COMMAND < phdos.in <http://phdos.in> > phdos.out
$ECHO " done "

$ECHO
$ECHO "$CURRENT_DIR: done"

-- 
=============================
Yi Kong
Department of MSE
Tsinghua University
PR China, 100084
=============================
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