[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>
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--
********************************************************
- 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>
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