[Pw_forum] XSpectra on graphite slab

Alain Allouche alain.allouche at univ-provence.fr
Wed Mar 16 17:02:18 CET 2011


Hi Derek,
Of course I have it taken from the XS example pseudo files, I used it  
first on the diamondh case (I just duplicate and adapted the data files)
Best
Alain

Le 16 mars 11 à 16:41, Derek Stewart a écrit :

> 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
> ** New Webpage **
> http://sites.google.com/site/dft4nano/
> 250 Duffield Hall
> Cornell Nanoscale Facility (CNF)
> Ithaca, NY 14853
> stewart (at) cnf.cornell.edu
> (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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