[Pw_forum] hydrogen adsorption on graphene

Eyvaz Isaev eyvaz_isaev at yahoo.com
Thu Jul 31 12:33:49 CEST 2008


Hi,

Please read carefully Troubleshootings in the UserGuide (page 55 or around). This is very very very ... famous question.

Bests,
Eyvaz.

 -------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com



----- Original Message ----
From: "s305igun at mail.chem.itb.ac.id" <s305igun at mail.chem.itb.ac.id>
To: wangxinquan at tju.edu.cn; PWSCF Forum <pw_forum at pwscf.org>
Sent: Thursday, July 31, 2008 11:55:55 AM
Subject: [Pw_forum] hydrogen adsorption on graphene

Dear PW_Forum

I need your help, I was calculated hydrogen adsorption on graphene layer
and this is my trouble output:

starting charge  281.99714, renormalised to  282.00000
     Starting wfc are  282 atomic wfcs

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #       296
     info =/= 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Would you like to explain to me about info =/= 0?

thanks very mach. and this is my input list:

#!/bin/bash

. ../environment_variables

PW_COMMAND=$PW_ROOT/bin/pw.x
PP_COMMAND=$PW_ROOT/bin/pp.x

##### Generate input files for scf calculation

cat <<EOF > h2-graphite.scf.in
&CONTROL
  calculation   = 'scf'
  title         = 'h2 / carbon layers slab - for demonstrative purposes only'
  restart_mode  = 'from_scratch'
  prefix        = 'h2-graphite'
  outdir        = '$TMP_DIR/'
  pseudo_dir    = '$PSEUDO_DIR/'
/
&SYSTEM
    ibrav     = 0,
    celldm(1) = 5.3d0
    nat       = 72
    ntyp      = 2
    ecutwfc   = 16.0d0
    ecutrho   = 160.0d0
    occupations = 'smearing'
    degauss     = 0.03D0
    smearing    = 'mp'
/
&ELECTRONS
    conv_thr    = 1.0d-5
    mixing_mode = 'plain'
    mixing_beta = 0.3d0
/
ATOMIC_SPECIES
C     12.0107  C.pbe-rrkjus.UPF
H      1.0079  H.pbe-rrkjus.UPF
ATOMIC_POSITIONS angstrom
H       8.741687    2.884450    1.000000
H       8.741715    2.884450    1.500000
C       1.249543   -0.711074    0.000000
C       0.000947   -0.016393    0.000000
C       0.000844    1.443145    0.000000
C       1.249381    2.159954    0.000000
C       1.249409    3.608946    0.000000
C       0.000843    4.325668    0.000000
C       0.000939    5.785283    0.000000
C       1.249515    6.479991    0.000000
C       1.249981   -1.825631    0.000000
C       1.249981    7.594413    0.000000
C       3.746978   -0.711074    0.000000
C       2.498382   -0.016393    0.000000
C       2.498279    1.443145    0.000000
C       3.746816    2.159954    0.000000
C       3.746844    3.608946    0.000000
C       2.498278    4.325668    0.000000
C       2.498374    5.785283    0.000000
C       3.746950    6.479991    0.000000
C       3.747416   -1.825631    0.000000
C       3.747416    7.594413    0.000000
C       6.244413   -0.711074    0.000000
C       4.995817   -0.016393    0.000000
C       4.995714    1.443145    0.000000
C       6.244251    2.159954    0.000000
C       6.244279    3.608946    0.000000
C       4.995713    4.325668    0.000000
C       4.995809    5.785283    0.000000
C       6.244385    6.479991    0.000000
C       6.244851   -1.825631    0.000000
C       6.244851    7.594413    0.000000
C       8.741849   -0.711074    0.000000
C       7.493253   -0.016393    0.000000
C       7.493150    1.443145    0.000000
C       8.741687    2.159954    0.000000
C       8.741715    3.608946    0.000000
C       7.493149    4.325668    0.000000
C       7.493245    5.785283    0.000000
C       8.741821    6.479991    0.000000
C       8.742287   -1.825631    0.000000
C       8.742287    7.594413    0.000000
C      11.239284   -0.711074    0.000000
C       9.990688   -0.016393    0.000000
C       9.990585    1.443145    0.000000
C      11.239122    2.159954    0.000000
C      11.239150    3.608946    0.000000
C       9.990584    4.325668    0.000000
C       9.990680    5.785283    0.000000
C      11.239256    6.479991    0.000000
C      11.239722   -1.825631    0.000000
C      11.239722    7.594413    0.000000
C      13.736719   -0.711074    0.000000
C      12.488123   -0.016393    0.000000
C      12.488020    1.443145    0.000000
C      13.736557    2.159954    0.000000
C      13.736585    3.608946    0.000000
C      12.488019    4.325668    0.000000
C      12.488115    5.785283    0.000000
C      13.736691    6.479991    0.000000
C      13.737157   -1.825631    0.000000
C      13.737157    7.594413    0.000000
C      16.234154   -0.711074    0.000000
C      14.985558   -0.016393    0.000000
C      14.985455    1.443145    0.000000
C      16.233992    2.159954    0.000000
C      16.234020    3.608946    0.000000
C      14.985454    4.325668    0.000000
C      14.985550    5.785283    0.000000
C      16.234126    6.479991    0.000000
C      16.234592   -1.825631    0.000000
C      16.234592    7.594413    0.000000
K_POINTS { automatic }
     2   1   1  1  1  1
CELL_PARAMETERS
   1.000000    0.000000    0.000000
   0.000000    1.144031    0.000000
   0.000000    0.000000    0.858023
EOF

cat <<EOF > h2.scf.in
&CONTROL
  calculation   = 'scf'
  title         = 'h2 - for demonstrative purposes only'
  restart_mode  = 'from_scratch'
  prefix        = 'h2'
  outdir        = '$TMP_DIR'
  pseudo_dir    = '$PSEUDO_DIR'
/
&SYSTEM
    ibrav     = 0,
    celldm(1) = 5.3d0
    nat       = 2
    ntyp      = 1
    ecutwfc   = 16.0d0
    ecutrho   = 160.0d0
    occupations = 'smearing'
    degauss     = 0.03D0
    smearing    = 'mp'
/
&ELECTRONS
    conv_thr    = 1.0d-5
    mixing_mode = 'plain'
    mixing_beta = 0.3d0
/
ATOMIC_SPECIES
H      1.0079  H.pbe-rrkjus.UPF
ATOMIC_POSITIONS angstrom
H       8.741687    2.884450    1.000000
H       8.741715    2.884450    1.500000
K_POINTS { automatic }
     2   2   1  1  1  1
CELL_PARAMETERS
   1.000000    0.000000    0.000000
   0.000000    1.144031    0.000000
   0.000000    0.000000    0.858023
EOF

cat <<EOF > graphite.scf.in
&CONTROL
  calculation   = 'scf'
  title         = 'graphite layers slab - for demonstrative purposes only'
  restart_mode  = 'from_scratch'
  prefix        = 'graphite'
  outdir        = '$TMP_DIR'
  pseudo_dir    = '$PSEUDO_DIR'
/
&SYSTEM
    ibrav     = 0,
    celldm(1) = 5.3d0
    nat       = 70
    ntyp      = 1
    ecutwfc   = 16.0d0
    ecutrho   = 160.0d0
    occupations = 'smearing'
    degauss     = 0.03D0
    smearing    = 'mp'
/
&ELECTRONS
    conv_thr    = 1.0d-5
    mixing_mode = 'plain'
    mixing_beta = 0.3d0
/
ATOMIC_SPECIES
C     12.0107  C.pbe-rrkjus.UPF
ATOMIC_POSITIONS angstrom
C       1.249543   -0.711074    0.000000
C       0.000947   -0.016393    0.000000
C       0.000844    1.443145    0.000000
C       1.249381    2.159954    0.000000
C       1.249409    3.608946    0.000000
C       0.000843    4.325668    0.000000
C       0.000939    5.785283    0.000000
C       1.249515    6.479991    0.000000
C       1.249981   -1.825631    0.000000
C       1.249981    7.594413    0.000000
C       3.746978   -0.711074    0.000000
C       2.498382   -0.016393    0.000000
C       2.498279    1.443145    0.000000
C       3.746816    2.159954    0.000000
C       3.746844    3.608946    0.000000
C       2.498278    4.325668    0.000000
C       2.498374    5.785283    0.000000
C       3.746950    6.479991    0.000000
C       3.747416   -1.825631    0.000000
C       3.747416    7.594413    0.000000
C       6.244413   -0.711074    0.000000
C       4.995817   -0.016393    0.000000
C       4.995714    1.443145    0.000000
C       6.244251    2.159954    0.000000
C       6.244279    3.608946    0.000000
C       4.995713    4.325668    0.000000
C       4.995809    5.785283    0.000000
C       6.244385    6.479991    0.000000
C       6.244851   -1.825631    0.000000
C       6.244851    7.594413    0.000000
C       8.741849   -0.711074    0.000000
C       7.493253   -0.016393    0.000000
C       7.493150    1.443145    0.000000
C       8.741687    2.159954    0.000000
C       8.741715    3.608946    0.000000
C       7.493149    4.325668    0.000000
C       7.493245    5.785283    0.000000
C       8.741821    6.479991    0.000000
C       8.742287   -1.825631    0.000000
C       8.742287    7.594413    0.000000
C      11.239284   -0.711074    0.000000
C       9.990688   -0.016393    0.000000
C       9.990585    1.443145    0.000000
C      11.239122    2.159954    0.000000
C      11.239150    3.608946    0.000000
C       9.990584    4.325668    0.000000
C       9.990680    5.785283    0.000000
C      11.239256    6.479991    0.000000
C      11.239722   -1.825631    0.000000
C      11.239722    7.594413    0.000000
C      13.736719   -0.711074    0.000000
C      12.488123   -0.016393    0.000000
C      12.488020    1.443145    0.000000
C      13.736557    2.159954    0.000000
C      13.736585    3.608946    0.000000
C      12.488019    4.325668    0.000000
C      12.488115    5.785283    0.000000
C      13.736691    6.479991    0.000000
C      13.737157   -1.825631    0.000000
C      13.737157    7.594413    0.000000
C      16.234154   -0.711074    0.000000
C      14.985558   -0.016393    0.000000
C      14.985455    1.443145    0.000000
C      16.233992    2.159954    0.000000
C      16.234020    3.608946    0.000000
C      14.985454    4.325668    0.000000
C      14.985550    5.785283    0.000000
C      16.234126    6.479991    0.000000
C      16.234592   -1.825631    0.000000
C      16.234592    7.594413    0.000000
K_POINTS { automatic }
     2   1   1  1  1  1
CELL_PARAMETERS
   1.000000    0.000000    0.000000
   0.000000    1.144031    0.000000
   0.000000    0.000000    0.858023
EOF

##### Input files generated. Now execute!

for PREFIX in graphite h2 h2-graphite; do
echo Now doing $PREFIX ...
$PW_COMMAND < $PREFIX.scf.in > $PREFIX.scf.out
cat <<EOF > $PREFIX.ppin
&inputPP
   prefix   = '$PREFIX'
   outdir   = '$TMP_DIR'
   filplot  = '$PREFIX.charge'
   plot_num = 0
/
EOF
$PP_COMMAND < $PREFIX.ppin > $PREFIX.ppout
done
echo Done

oke everybody, thanks for your help

best regards

Rahmat Gunawan
Students of Chemistry Dept.
Lab of Theoretical and Computational Chemistry
Faculty of Mathematics and Natural Sciences
Bandung Institute of Technology
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