[Pw_forum] XSpectra on graphite slab

Derek Stewart stewart at cnf.cornell.edu
Wed Mar 16 16:41:44 CET 2011


Hi Alain,

A quick question on your problem with the Ch atom.  Did you have the 
corresponding pseudopotential, "Ch_PBE_TM_2pj.UPF" in the pseudo directory?

Best regards,

Derek



################################
Derek Stewart, Ph. D.
Senior Research Associate
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(607) 255-2856



On 3/16/2011 11:22 AM, Alain Allouche wrote:
> 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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