[Pw_forum] Charge Density of the Graphene-Lithium System

[Thaneshwor Kaloni]

Dear Gulcin,

Please run three scf in three different out directory like as,
1) graphene+Li
2)graphene
3)Li

Then run three post processing by pp.x
1) graphene+Li
2)graphene
3)Li

Then, run a final post processing by pp.x
The final input looking  like one pasted below,

 &inputpp
/
&plot
nfile=3
filepp(1)='all.charge'
filepp(2)='Li.charge'
filepp(3)='graphene.charge'
weight(1)=1
weight(2)=-1
weight(3)=-1
iflag=3
output_format=5
fileout='chden.xsf'
/

Finally, plot chden.xsf file.
I hope it will help you.

Kaloni

KAUST, KSA



Message: 6
Date: Fri, 6 Jul 2012 12:42:23 -0400
From: Gulcin Kucukdalyan <gkucukdalyan at gmail.com>
Subject: [Pw_forum] Charge Density of the Graphene-Lithium System
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
        <CAOwUK0BbefkXzwtcfP106gFa3mEBQqOUtcW9MKjGNMRkJJZH9Q at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi All,

I am trying to calculate the charge density of the graphene -lithium system
by showing the negative and positive regions on it. When i uploaded the
below input file to Xcrysden i cannnot see  either  the negative and
positive regions  nor  the charge flow on 3D Xccrysden figure. How should i
modify my file to do so?

Thansk in advance,

Gulcin

# self-consistent calculation
    cat > gli.scf.in << EOF
 &control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='gli',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system
    ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
    ecutwfc =60.0,
    ecutrho = 500.0
 occupations='smearing', smearing='methfessel-paxton', degauss=0.02
 /
 &electrons
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-7
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-rrkjus.UPF
 Li  6.9142   Li.pz-n-vbc.UPF
ATOMIC_POSITIONS
C       -0.000169177  -0.000292351   0.000000000
C        0.333413183  -0.000292351   0.000000000
C        0.500204479   0.288597992   0.000000000
C        0.333413183   0.577488334   0.000000000
C       -0.000169177   0.577488334   0.000000000
C       -0.166960373   0.288597992   0.000000000
Li       0.166621953   0.288597992   0.416524683
K_POINTS AUTOMATIC
5 5 6 0 0 0
EOF
    $ECHO "  running the scf calculation for Gr-Li...\c"
    $PW_COMMAND < gli.scf.in > gli.scf.out
    check_failure $?
    $ECHO " done"

# post-processing for charge density
cat > gli.pp.in << EOF
   &inputpp
   prefix  = 'gli'
   outdir = '$TMP_DIR/'
   filplot = 'gli.pp'
   plot_num= 7
   kpoint = 1
   kband = 14
   spin_component = 0

/

 &plot
    nfile = 1
    filepp(1) = 'gli.pp'
    weight(1) = 1.0
    iflag = 3
    output_format = 5
    fileout = 'gli.xsf'
    /
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