[Pw_forum] XSpectra on graphite slab

Alain Allouche alain.allouche at univ-provence.fr
Wed Mar 16 16:22:44 CET 2011


Dear Espressionists,
I tried to run the diamond example in espresso-4.2-examples/examples/ 
XSpectra_example and it works fine using espresso-4.2. Threfore I  
duplicated the diamond files to make the calculation on graphite and  
the input looks like:

  &control
     calculation='scf'
     restart_mode='from_scratch',
!   restart_mode='restart',
!   pseudo_dir = '/Users/allouche/pseudo_espresso/'
!   pseudo_dir = '/homegpfs/rech/ams/rams001/pseudo_espresso/'
     pseudo_dir = '/home/allouche/pseudo_espresso'
     prefix='graphite'
  /
  &system
     ibrav = 4
     a =9.880,
     b =9.880,
     c =20.0000
     cosab = 0.0
     cosac = 0.0
     cosbc = -0.5
     nat= 64
     ntyp= 2,
     ecutwfc=40.
     tot_charge=+1.0,
     degauss=0.001
     nspin = 1
     london=.true.
  /
  &electrons
     mixing_beta = 0.3,
     startingwfc = 'file'
  /
ATOMIC_SPECIES
C 12 C_PBE_TM_2pj.UPF
Ch 12 Ch_PBE_TM_2pj.UPF
ATOMIC_POSITIONS crystal
Ch 0.166589 0.083384 0.827761
C 0.249912 0.250043 0.827591
C 0.333380 0.166614 0.665253
C 0.250046 0.249946 0.665282
C 0.166590 0.333382 0.827797
C 0.249927 0.500060 0.827753
C 0.333381 0.416617 0.665261
C 0.250049 0.499953 0.665288
C 0.166617 0.583430 0.827809
C 0.249925 0.750054 0.827751
C 0.333382 0.666616 0.665260
C 0.250048 0.749950 0.665286
C 0.166616 0.833367 0.827787
C 0.249927 0.000045 0.827690
C 0.333384 0.916617 0.665257
C 0.250048 0.999946 0.665282
C 0.416586 0.083370 0.827522
C 0.499907 0.250007 0.827142
C 0.583384 0.166614 0.665248
C 0.500045 0.249945 0.665274
C 0.416562 0.333369 0.827235
C 0.499907 0.500070 0.827236
C 0.583381 0.416619 0.665246
C 0.500048 0.499951 0.665283
C 0.416589 0.583393 0.827627
C 0.499919 0.750051 0.827751
C 0.583381 0.666616 0.665259
C 0.500046 0.749950 0.665287
C 0.416552 0.833366 0.827806
C 0.499916 0.000042 0.827678
C 0.583386 0.916617 0.665253
C 0.500047 0.999947 0.665279
C 0.666599 0.083383 0.827729
C 0.749937 0.250040 0.827505
C 0.833385 0.166614 0.665243
C 0.750051 0.249946 0.665273
C 0.666613 0.333368 0.827149
C 0.749971 0.500070 0.827145
C 0.833384 0.416616 0.665248
C 0.750053 0.499953 0.665273
C 0.666611 0.583417 0.827236
C 0.749935 0.750067 0.827591
C 0.833383 0.666618 0.665251
C 0.750054 0.749954 0.665279
C 0.666599 0.833390 0.827795
C 0.749964 0.000070 0.827829
C 0.833383 0.916619 0.665245
C 0.750052 0.999950 0.665271
C 0.916596 0.083383 0.827854
C 0.999910 0.250017 0.827831
C 0.083378 0.166616 0.665246
C 0.000049 0.249946 0.665273
C 0.916598 0.333382 0.827732
C 0.999937 0.500062 0.827682
C 0.083381 0.416612 0.665255
C 0.000052 0.499951 0.665280
C 0.916611 0.583397 0.827525
C 0.999932 0.750051 0.827692
C 0.083381 0.666615 0.665256
C 0.000052 0.749950 0.665280
C 0.916597 0.833392 0.827762
C 0.999909 0.000071 0.827828
C 0.083381 0.916617 0.665250
C 0.000050 0.999949 0.665269
K_POINTS Automatic
6 6 1  0 0 0

FIRST PROBLEM: expresso-4.2 and 4.1 do not like atom Ch (they did for  
diamond):

      This program is part of the open-source Quantum ESPRESSO suite
      for quantum simulation of materials; please cite
          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502  
(2009);
           URL http://www.quantum-espresso.org",
      in publications or presentations arising from this work. More  
details at
      http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

      Parallel version (MPI), running on    40 processors
      K-points division:     npool     =   20
      R & G space division:  proc/pool =    2

      Current dimensions of program PWSCF are:
      Max number of different atomic species (ntypx) = 10
      Max number of k-points (npk) =  40000
      Max angular momentum in pseudopotentials (lmaxx) =  3
      Waiting for input...
Atom Ch not found
rank 0 in job 1  node07_41087   caused collective abort of all ranks
   exit status of rank 0: killed by signal 9


Only espresso-4.0.4 did like !!! so I tried it on diamond (for  
checking) and then on graphite again, it works

SECOND PROBLEM:
The data for XSpectra:
  &input_xspectra
     calculation='fermi_level',
     prefix='graphite',
     xread_wf=.true.,
     xiabs=1
  /
  &plot
  /
  &pseudos
     filecore='C.wfc',
  /
  &cut_occ
  /
6 6 1  0 0 0


The result:


      Program XSPECTRA v.4.2.1   starts on 16Mar2011 at 15:52:46

      This program is part of the open-source Quantum ESPRESSO suite
      for quantum simulation of materials; please acknowledge
          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502  
(2009);
           URL http://www.quantum-espresso.org",
      in publications or presentations arising from this work. More  
details at
      http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

      Parallel version (MPI), running on    40 processors
      R & G space division:  proc/pool =   40
  bef

      Planes per process (thick) : nr3 = 160 npp =    4 ncplane =  6400

      Proc/  planes cols     G    planes cols    G      columns  G
      Pool       (dense grid)       (smooth grid)      (wavefct grid)
         1     4     96     9750    4     96     9750     26     1358
         2     4     96     9750    4     96     9750     26     1356
         3     4     96     9750    4     96     9750     26     1356
         4     4     96     9750    4     96     9750     26     1356
         5     4     96     9750    4     96     9750     26     1356
         6     4     96     9750    4     96     9750     26     1356
         7     4     96     9748    4     96     9748     26     1356
         8     4     96     9748    4     96     9748     26     1352
         9     4     96     9750    4     96     9750     25     1347
        10     4     96     9750    4     96     9750     26     1356
        11     4     96     9750    4     96     9750     26     1356
        12     4     96     9750    4     96     9750     26     1356
        13     4     96     9750    4     96     9750     26     1356
        14     4     97     9753    4     97     9753     26     1356
        15     4     97     9753    4     97     9753     26     1356
        16     4     96     9748    4     96     9748     26     1350
        17     4     96     9748    4     96     9748     26     1350
        18     4     96     9748    4     96     9748     26     1350
        19     4     96     9748    4     96     9748     26     1350
        20     4     96     9748    4     96     9748     26     1350
        21     4     96     9748    4     96     9748     26     1350
        22     4     96     9748    4     96     9748     26     1350
        23     4     96     9748    4     96     9748     26     1350
        24     4     96     9748    4     96     9748     26     1350
        25     4     96     9748    4     96     9748     26     1350
        26     4     97     9751    4     97     9751     26     1350
        27     4     97     9751    4     97     9751     26     1358
        28     4     97     9751    4     97     9751     26     1358
        29     4     97     9751    4     97     9751     26     1358
        30     4     97     9751    4     97     9751     26     1356
        31     4     97     9751    4     97     9751     26     1356
        32     4     97     9751    4     97     9751     26     1356
        33     4     97     9751    4     97     9751     26     1356
        34     4     97     9751    4     97     9751     26     1356
        35     4     97     9751    4     97     9751     26     1356
        36     4     97     9751    4     97     9751     26     1356
        37     4     96     9748    4     96     9748     26     1356
        38     4     96     9748    4     96     9748     26     1356
        39     4     96     9748    4     96     9748     26     1356
        40     4     96     9748    4     96     9748     26     1356
      tot    160   3853   389985  160   3853   389985   1039    54169

  af

  Approx. ram memory needed per proc in MB =   1.482000000000000E-003

  k-points : nkstot=          20
  -------------- Crystal Structure ------------
  celldm(1:6)
    18.67049419    1.00000000    2.02429150
     0.00000000    0.00000000    0.00000000
  direct lattice vectors
     1.00000000   -0.50000000    0.00000000
     0.00000000    0.86602540    0.00000000
     0.00000000    0.00000000    2.02429150
  reciprocal lattice vectors
     1.00000000    0.00000000    0.00000000
     0.57735027    1.15470054    0.00000000
     0.00000000    0.00000000    0.49400000
  nks=          20  nkstot=          20
   ----k-point list [units 2*pi/celldm(1)], weight---------
      1    0.00000000    0.00000000    0.00000000    0.05555556
      2    0.00000000    0.19245009    0.00000000    0.11111111
      3    0.00000000    0.38490018    0.00000000    0.11111111
      4    0.00000000   -0.57735027    0.00000000    0.05555556
      5    0.16666667    0.28867513    0.00000000    0.11111111
      6    0.16666667    0.48112522    0.00000000    0.11111111
      7    0.33333333    0.57735027    0.00000000    0.11111111
      8   -0.16666667    0.09622504    0.00000000    0.11111111
      9    0.16666667    0.09622504    0.00000000    0.11111111
     10   -0.33333333    0.19245009    0.00000000    0.11111111
     11    0.33333333    0.19245009    0.00000000    0.11111111
     12    0.50000000   -0.28867513    0.00000000    0.05555556
     13   -0.50000000   -0.28867513    0.00000000    0.05555556
     14   -0.16666667    0.28867513    0.00000000    0.11111111
     15    0.33333333    0.00000000    0.00000000    0.11111111
     16   -0.16666667    0.48112522    0.00000000    0.11111111
     17   -0.33333333    0.38490018    0.00000000    0.11111111
     18    0.50000000    0.09622504    0.00000000    0.11111111
     19   -0.33333333   -0.38490018    0.00000000    0.11111111
     20    0.50000000   -0.09622504    0.00000000    0.11111111
  -------------------------------------------------
  --- Polarisation and k vector [cartesian coordinates]----
xepsilon(:)= 1.00000000 0.00000000 0.00000000
xkvec(:)= 1.00000000 0.00000000 0.00000000

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%%%%%%%%%
      from main program : error #        63
      Wrong xiabs!!!
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%%%%%%%%%

      stopping ...
rank 30 in job 1  node08_33288   caused collective abort of all ranks
   exit status of rank 30: killed by signal 9
rank 25 in job 1  node08_33288   caused collective abort of all ranks
   exit status of rank 25: killed by signal 9
rank 15 in job 1  node08_33288   caused collective abort of all ranks
   exit status of rank 15: killed by signal 9
rank 0 in job 1  node08_33288   caused collective abort of all ranks
   exit status of rank 0: killed by signal 9


Can somebody explain me the curious behavior of pw.x accepting Ch on  
diamond and not on graphite, and  this "Wrong xiabs!!!" ??

Thank you in advance



  Dr. Alain ALLOUCHE
  Physique des Interactions Ioniques et   Moleculaires
  CNRS / Universite de Provence
  Campus Saint Jerome Service 242
  Avenue de l'Escadrille Normandie-Niemen
  13397 Marseille Cedex 20 - France
  Tel : +33 (0)  4 91 28 85 76
  Mobile:+33 681 84 80 66
  Fax : +33 491.28.89.05
  email: Alain.Allouche at univ-provence.fr










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