[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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