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

Layla Martin-Samos lmartinsamos at gmail.com
Mon Apr 18 09:04:59 CEST 2011


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.
>>
>> --
>> ********************************************************
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>> ********************************************************
>>
>>    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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>
>
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