[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
** 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
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
More information about the users
mailing list