[QE-users] Calculations with van der Waals correction stopped with an error

Paolo Giannozzi p.giannozzi at gmail.com
Thu Apr 8 16:23:58 CEST 2021


QE uses the last available version of DFT-D3 (v.3.2, 2016) and all
functionals implemented there can be used as long as one translates the
name used in QE into the name used in DFT-D3

On Thu, Apr 8, 2021 at 3:15 PM Michal Krompiec <michal.krompiec at gmail.com>
wrote:

> Hi Jibiao,
> You can also add DFT-D3 or DFT-D4 corrections using ASE, see
> https://wiki.fysik.dtu.dk/ase/ase/calculators/dftd3.html and
> https://github.com/dftd4/dftd4/tree/main/python
> Thus you won't be limited by the parameters from QE but can use any
> functional parametrized in the official DFTD3 and DFTD4 codes.
>
> Best regards,
> Michal Krompiec, Merck Electronics
>
> On Thu, 8 Apr 2021 at 09:37, Jibiao Li <jibiaoli at foxmail.com> wrote:
>
>> Hi, All
>>
>> My NEB calculations with the the parameters below go smoothly
>>                     vdw_corr = 'grimme-d2' ,
>> but when I tried to perform NEB calculations with the following parameters
>>                     vdw_corr = 'grimme-d3' ,
>> but the program stopped and gave the error below. The input file is
>> listed. How should I resolve this problem?
>>
>>
>>      Program NEB v.6.7MaX starts on  8Apr2021 at 16:15:41
>>
>>      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);
>>          "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>>           URL http://www.quantum-espresso.org",
>>      in publications or presentations arising from this work. More
>> details at
>>      http://www.quantum-espresso.org/quote
>>
>>      Parallel version (MPI), running on    24 processors
>>
>>      MPI processes distributed on     1 nodes
>>      R & G space division:  proc/nbgrp/npool/nimage =      24
>>
>>      parsing_file_name: hdw.neb.inp
>>      Reading input from pw_1.in
>>      file O.pbe-n-kjpaw_psl.0.1.UPF: wavefunction(s)  2P renormalized
>>      file H.pbe-kjpaw_psl.0.1.UPF: wavefunction(s)  1S renormalized
>>      file Pd.pbe-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S 4D
>> renormalized
>>
>>      IMPORTANT: XC functional enforced from input :
>>      Exchange-correlation= SLA+PW+OBK8+P86
>>                            (   1   4  23   1   0   0   0)
>>      Any further DFT definition will be discarded
>>      Please, verify this is what you really want
>>
>>
>>      --------------------------------------------
>>      Parameters for DFT-D3 Dispersion Correction:
>>      --------------------------------------------
>>        Reference C6 values for interpolation:
>>
>>          atom   Coordination number   C6
>>          H          0.912             6.05
>>          H          0.000            15.18
>>          O          0.000            31.01
>>          O          0.993            25.63
>>          O          1.989            20.74
>>          Pd         0.000          1217.01
>>          Pd         1.863           573.90
>>          Pd         5.710           531.75
>>
>>        Values used:
>>
>>          atom   Coordination number  R0_AB[au]  C6      C8
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>  program stopped due to: functional name unknown
>>
>>
>> BEGIN
>> BEGIN_PATH_INPUT
>> &PATH
>>   restart_mode      = 'from_scratch',
>>   string_method     = 'neb',
>>   nstep_path        = 198,
>>   ds                = 1.D0,
>>   opt_scheme        = 'broyden',
>>   first_last_opt    = .TRUE.,
>>   num_of_images     = 11,
>>   k_max             = 0.6D0,
>>   k_min             = 0.6D0,
>>   CI_scheme         = 'auto',
>> /
>> END_PATH_INPUT
>> BEGIN_ENGINE_INPUT
>> &CONTROL
>>   prefix         = 'hdw',
>>   outdir         = './',
>>                   pseudo_dir = '/GFPS8p/shn003/pseudo' ,
>> /
>> &SYSTEM
>>                        ibrav = 4,
>>                    celldm(1) = 15.929830662,
>>                    celldm(3) = 3.30768592,
>>                          nat = 39,
>>                         ntyp = 3,
>>                      ecutwfc = 49 ,
>>                      ecutrho = 411 ,
>>                  occupations = 'smearing' ,
>>                      degauss = 0.05D0 ,
>>                     smearing = 'methfessel-paxton' ,
>>                    input_dft = 'sla+pw+obk8+p86',
>>                     vdw_corr = 'grimme-d3' ,
>> /
>> &ELECTRONS
>>              electron_maxstep = 299,
>>                  mixing_beta = 0.2D0 ,
>>              diagonalization = 'david' ,
>> /
>> ATOMIC_SPECIES
>>     O   15.999  O.pbe-n-kjpaw_psl.0.1.UPF
>>     H   1.0079  H.pbe-kjpaw_psl.0.1.UPF
>>    Pd   106.40  Pd.pbe-n-kjpaw_psl.1.0.0.UPF
>> BEGIN_POSITIONS
>> FIRST_IMAGE
>> ATOMIC_POSITIONS angstrom
>> H             0.7732521867        5.6371760314        9.3289503919
>> H             0.7722698171        4.0982334506        9.3278512343
>> O             0.1715563890        4.8680942596        9.3464327196
>> Pd           -0.0175303681        0.0015594779        6.8768483733
>> Pd           -2.8551417192        4.8682296408        6.8675496435
>> Pd            5.6035594783        0.0006419052        6.8717368298
>> Pd            2.7834297962        4.8677192832        6.8728695609
>> Pd           -1.4291971180        2.4166870853        6.8690467718
>> Pd            4.1976043804        2.4331824206        6.8747983066
>> Pd            1.3886481901        2.4344928528        6.8708652939
>> Pd            2.7837857999        0.0188620972        6.8682659097
>> Pd           -0.0551097945        4.8683868875        6.8741603609
>> Pd            0.0000000000        0.0000000000        0.0000000000    0
>> 0   0
>> Pd           -2.8099009270        4.8668911700        0.0000000000    0
>> 0   0
>> Pd            5.6198018540        0.0000000000        0.0000000000    0
>> 0   0
>> Pd            2.8099009270        4.8668911700        0.0000000000    0
>> 0   0
>> Pd            2.8099009270        1.6222970570        2.2942745000    0
>> 0   0
>> Pd            0.0000000000        6.4891882270        2.2942745000    0
>> 0   0
>> Pd            0.0000000000        3.2445941130        4.5885489990    0
>> 0   0
>> Pd            5.6198018540        3.2445941130        4.5885489990    0
>> 0   0
>> Pd           -1.4049504640        2.4334455850        0.0000000000    0
>> 0   0
>> Pd            4.2148513910        2.4334455850        0.0000000000    0
>> 0   0
>> Pd            1.4049504640        4.0557426420        2.2942745000    0
>> 0   0
>> Pd            1.4049504640        0.8111485280        4.5885489990    0
>> 0   0
>> Pd           -1.4049504640        5.6780396980        4.5885489990    0
>> 0   0
>> Pd            7.0247523180        0.8111485280        4.5885489990    0
>> 0   0
>> Pd            4.2148513910        5.6780396980        4.5885489990    0
>> 0   0
>> Pd            1.4049504640        2.4334455850        0.0000000000    0
>> 0   0
>> Pd           -1.4049504640        4.0557426420        2.2942745000    0
>> 0   0
>> Pd            4.2148513910        4.0557426420        2.2942745000    0
>> 0   0
>> Pd            4.2148513910        0.8111485280        4.5885489990    0
>> 0   0
>> Pd            1.4049504640        5.6780396980        4.5885489990    0
>> 0   0
>> Pd            2.8099009270        0.0000000000        0.0000000000    0
>> 0   0
>> Pd           -0.0000000000        4.8668911700        0.0000000000    0
>> 0   0
>> Pd           -0.0000000000        1.6222970570        2.2942745000    0
>> 0   0
>> Pd           -2.8099009270        6.4891882270        2.2942745000    0
>> 0   0
>> Pd            5.6198018540        1.6222970570        2.2942745000    0
>> 0   0
>> Pd            2.8099009270        6.4891882270        2.2942745000    0
>> 0   0
>> Pd            2.8099009270        3.2445941130        4.5885489990    0
>> 0   0
>> LAST_IMAGE
>> ATOMIC_POSITIONS angstrom
>> H             3.4499239762        5.6377348817        9.3260575484
>> H             3.4408583460        4.0977051737        9.3250953653
>> O             2.8668984993        4.8680459378        9.3454755033
>> Pd            0.0256278270        0.0192486174        6.8685945671
>> Pd           -2.7640583908        4.8681895736        6.8679430776
>> Pd            5.6360027054        0.0000461678        6.8719390616
>> Pd            2.8668984993        4.8685434926        6.8743573252
>> Pd           -1.3880054506        2.4331683556        6.8752198973
>> Pd            4.2389485839        2.4161707141        6.8693749593
>> Pd            1.4208524299        2.4351327258        6.8711300023
>> Pd            2.8272497162        0.0014869205        6.8772505637
>> Pd            0.0271545824        4.8675853735        6.8731795722
>> Pd            0.0000000000        0.0000000000        0.0000000000    0
>> 0   0
>> Pd           -2.8099009270        4.8668911700        0.0000000000    0
>> 0   0
>> Pd            5.6198018540        0.0000000000        0.0000000000    0
>> 0   0
>> Pd            2.8099009270        4.8668911700        0.0000000000    0
>> 0   0
>> Pd            2.8099009270        1.6222970570        2.2942745000    0
>> 0   0
>> Pd           -0.0000000000        6.4891882270        2.2942745000    0
>> 0   0
>> Pd            0.0000000000        3.2445941130        4.5885489990    0
>> 0   0
>> Pd            5.6198018540        3.2445941130        4.5885489990    0
>> 0   0
>> Pd           -1.4049504640        2.4334455850        0.0000000000    0
>> 0   0
>> Pd            4.2148513910        2.4334455850        0.0000000000    0
>> 0   0
>> Pd            1.4049504640        4.0557426420        2.2942745000    0
>> 0   0
>> Pd            1.4049504640        0.8111485280        4.5885489990    0
>> 0   0
>> Pd           -1.4049504640        5.6780396980        4.5885489990    0
>> 0   0
>> Pd            7.0247523180        0.8111485280        4.5885489990    0
>> 0   0
>> Pd            4.2148513910        5.6780396980        4.5885489990    0
>> 0   0
>> Pd            1.4049504640        2.4334455850        0.0000000000    0
>> 0   0
>> Pd           -1.4049504640        4.0557426420        2.2942745000    0
>> 0   0
>> Pd            4.2148513910        4.0557426420        2.2942745000    0
>> 0   0
>> Pd            4.2148513910        0.8111485280        4.5885489990    0
>> 0   0
>> Pd            1.4049504640        5.6780396980        4.5885489990    0
>> 0   0
>> Pd            2.8099009270        0.0000000000        0.0000000000    0
>> 0   0
>> Pd            0.0000000000        4.8668911700        0.0000000000    0
>> 0   0
>> Pd            0.0000000000        1.6222970570        2.2942745000    0
>> 0   0
>> Pd           -2.8099009270        6.4891882270        2.2942745000    0
>> 0   0
>> Pd            5.6198018540        1.6222970570        2.2942745000    0
>> 0   0
>> Pd            2.8099009270        6.4891882270        2.2942745000    0
>> 0   0
>> Pd            2.8099009270        3.2445941130        4.5885489990    0
>> 0   0
>> END_POSITIONS
>> K_POINTS automatic
>>   4 4 1   0 0 0
>> END_ENGINE_INPUT
>> END
>>
>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users



-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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