[Pw_forum] problems with input_dft='vdW-DF' in neb.x calculations

Giuseppe Mattioli giuseppe.mattioli at mlib.ism.cnr.it
Mon Apr 18 10:52:59 CEST 2011


Dear Layla
Thank you!
It works fine.
Giuseppe

On Monday 18 April 2011 09:04:59 Layla Martin-Samos wrote:
> In kernel table I change at line 172
> allocate(...) with if(.not. allocated) allocate
>
>     if(.not.allocated(q_mesh)) allocate( q_mesh(Nqs) )
>     if(.not.allocated(kernel)) allocate( kernel(0:Nr_points,Nqs,Nqs))
>     if(.not.allocated(d2phi_dk2)) allocate(d2phi_dk2(0:Nr_points,Nqs,Nqs) )
>
> you can download the svn version of the routines or change it by hand.
>
> (neb calls n_input_image times the read input routines of pwscf, so it was
> trying to allocate an object that was already allocated).
>
>
> bests
>
> Layla
>
>
> 2011/4/18 Layla Martin-Samos <lmartinsamos at gmail.com>
>
> > Dear Giuseppe, the problem allocating the object is probably related to
> > some "unexistent" deallocation. I'll take a look I give you a more
> > precise answer.
> >
> > bests
> >
> > Layla
> >
> >
> > 2011/4/16 Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
> >
> >> Dear all
> >> I'm facing a strange problem when performing neb.x calculations with the
> >> input_dft='vdW-DF' flag.
> >> I've tried the very same calculation (same machine, same QE 4.3
> >> version...)
> >> but for the vdW, e.g., in the case of cyclohexane isomerization (input
> >> files
> >> below). Everything is fine in the non-corrected case. On the contrary,
> >> this
> >> is the only standard output in the vdW case:
> >>
> >>      Program NEB v.4.3          starts on 16Apr2011 at 14:14: 6
> >>
> >>     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     8 processors
> >>     R & G space division:  proc/pool =    8
> >> Warning: card   &IONS ignored
> >> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      ION_DYNAMICS='BFGS' ignored
> >> Warning: card   / ignored
> >>
> >>     XC functional enforced from input :
> >>     Exchange-correlation      = VDW-DF (1449)
> >>     EXX-fraction              =        0.00
> >>     !!! Any further DFT definition will be discarded
> >>     !!! Please, verify this is what you really want !
> >>
> >> Warning: card   &IONS ignored
> >> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      ION_DYNAMICS='BFGS' ignored
> >> Warning: card   / ignored
> >>
> >>     XC functional enforced from input :
> >>     Exchange-correlation      = VDW-DF (1449)
> >>     EXX-fraction              =        0.00
> >>     !!! Any further DFT definition will be discarded
> >>     !!! Please, verify this is what you really want !
> >>
> >> and this is the reported system error:
> >>
> >> "kernel_table.f90", line 172: 1525-108 Error encountered while
> >> attempting to
> >> allocate a data object.  The program will stop.
> >>
> >> vdW calculations run of course without problems in standard pw.x jobs.
> >> A look at the above file has not provided any enlightenment (at least to
> >> me...)
> >>
> >> A minor question: why are the following printed in the standard output
> >> file?
> >> Warning: card   &IONS ignored
> >> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      ION_DYNAMICS='BFGS' ignored
> >> Warning: card   / ignored
> >> I followed the run_example template in the QE/examples/example17
> >> directory which contains the cards
> >> &IONS
> >>  pot_extrapolation = "second_order",
> >>  wfc_extrapolation = "second_order",
> >> /
> >>
> >> A further minor question: where can I found any documentation to set up
> >> a smd
> >> calculation using cards like:
> >> BEGIN_PATH_INPUT
> >> &PATH
> >>  string_method     = 'smd',
> >>  opt_scheme        = "langevin",
> >>  temp_req          = 200.0
> >> /
> >> END_PATH_INPUT
> >> BEGIN_ENGINE_INPUT
> >>
> >> Any comment or suggestion?
> >> Thank you in advance
> >> Giuseppe
> >>
> >> This is the one which works fine:
> >>
> >> export FILE="test"
> >> export INPFILE=$FILE-1.inp
> >> export OUTFILE=$FILE-1.out
> >> echo " $FILE"
> >> echo " $INPFILE"
> >> echo " $OUTFILE"
> >>
> >> cat > $INPFILE << EOF
> >> BEGIN
> >> BEGIN_PATH_INPUT
> >> &PATH
> >>  restart_mode      = 'from_scratch',
> >>  string_method     = 'neb',
> >>  nstep_path        = 200,
> >>  ds                = 2.D0,
> >>  opt_scheme        = "broyden",
> >>  num_of_images     = 9,
> >>  CI_scheme         = "no-CI",
> >>  path_thr          = 0.1D0,
> >> /
> >> END_PATH_INPUT
> >> BEGIN_ENGINE_INPUT
> >>  &CONTROL
> >>    prefix='$FILE',
> >>    pseudo_dir = '$PSEUDO_DIR/',
> >>    outdir='$TMP_DIR/',
> >>  /
> >>  &SYSTEM
> >>    ibrav=1, celldm(1)=20.0000
> >>    nat=18, ntyp=2,
> >>    ecutwfc = 25.0,
> >>    ecutrho = 200.0,
> >>    occupations='smearing', degauss=0.01,
> >>    nspin=1,
> >>  /
> >>  &ELECTRONS
> >>    mixing_mode='plain'
> >>    mixing_beta=0.2
> >>    conv_thr=1.0d-8
> >>    electron_maxstep=200
> >>  /
> >>  &IONS
> >>    pot_extrapolation = "second_order",
> >>    wfc_extrapolation = "second_order",
> >>    ion_dynamics='bfgs'
> >>  /
> >> ATOMIC_SPECIES
> >> C    12.011     C_pbe.van.UPF
> >> H     1.008     H_pbe.van.UPF
> >> BEGIN_POSITIONS
> >> FIRST_IMAGE
> >> ATOMIC_POSITIONS {angstrom}
> >> C        6.098316160   3.760656270   4.654408584
> >> C        5.535560000   5.029242896   4.000000000
> >> C        5.535560000   2.491939382   4.000000000
> >> C        4.000840929   5.027202726   4.000000000
> >> C        4.000950457   2.493714962   4.000000000
> >> C        3.441730882   3.760373055   3.339304890
> >> H        5.825930677   3.760664232   5.733651283
> >> H        7.207790908   3.760649901   4.611224167
> >> H        5.898266497   5.087596300   2.948897106
> >> H        5.921942861   5.933612152   4.514551016
> >> H        5.898578752   2.433310631   2.949074312
> >> H        5.922060506   1.587859796   4.515020902
> >> H        3.637454955   2.444160918   5.051149794
> >> H        3.611787526   1.587642834   3.490637392
> >> H        3.637077165   5.076985202   5.050984568
> >> H        3.611543166   5.933006456   3.490221051
> >> H        2.332375720   3.760276416   3.383439061
> >> H        3.714361008   3.760355870   2.259592492
> >> LAST_IMAGE
> >> ATOMIC_POSITIONS {angstrom}
> >> C        6.121592696   3.760535885   4.641499347
> >> C        5.535560000   5.025712602   4.000000000
> >> C        5.535560000   2.495388270   4.000000000
> >> C        3.977918610   5.023959085   4.000000000
> >> C        3.977930112   2.497154140   4.000000000
> >> C        3.393609861   3.760551962   4.644872629
> >> H        5.913189538   3.760513868   5.732562614
> >> H        7.227121303   3.760507977   4.543954834
> >> H        5.908541836   5.092099491   2.955785191
> >> H        5.923102018   5.926437334   4.518072829
> >> H        5.908479393   2.429064594   2.955753950
> >> H        5.923126757   1.594603868   4.517936370
> >> H        3.590403695   1.596442101   4.516411429
> >> H        3.603091688   2.435078428   2.956089377
> >> H        3.590454294   5.924681359   4.516455545
> >> H        3.603071258   5.086031218   2.956078488
> >> H        3.602033618   3.760529459   5.735973241
> >> H        2.288228742   3.760541827   4.546696293
> >> END_POSITIONS
> >> K_POINTS {gamma}
> >> END_ENGINE_INPUT
> >> END
> >> EOF
> >> $PARA_PREFIX $ESPRESSO/neb.x -inp $INPFILE >> $OUTFILE
> >>
> >> if I only add input_dft='vdW-DF' in the &SYSTEM list it does not work
> >> anymore.
> >>
> >> --
> >> ********************************************************
> >> - Article premier - Les hommes naissent et demeurent
> >> libres et ègaux en droits. Les distinctions sociales
> >> ne peuvent être fondèes que sur l'utilitè commune
> >> - Article 2 - Le but de toute association politique
> >> est la conservation des droits naturels et
> >> imprescriptibles de l'homme. Ces droits sont la libertè,
> >> la propriètè, la sùretè et la rèsistance à l'oppression.
> >> ********************************************************
> >>
> >>    Giuseppe Mattioli
> >>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> >>    v. Salaria Km 29,300 - C.P. 10
> >>    I 00015 - Monterotondo Stazione (RM)
> >>    Tel + 39 06 90672836 - Fax +39 06 90672316
> >>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ègaux en droits. Les distinctions sociales
ne peuvent être fondèes que sur l'utilitè commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libertè,
la propriètè, la sùretè et la rèsistance à l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00015 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>


More information about the Pw_forum mailing list