[QE-users] calculation of open-shell molecules (radicals) on top of metal surfaces

[Paolo Costa]

Dear QE users,

I want to calculate the affinity (ads. energy) between an open-shell
molecule (radical) and Pd(111) slab.
I have already computed a three layer Pd surface (72 Pd atoms) with and
without spin polarization (SP). The final energy differs from each other's
since a total magnetization of 20.61 Bohr mag/cell has been computed when
SP is included.

How can I calculate an open-shell molecule on top of such Pd slab? Can I
constrain the total magnetization to 1?

Any suggestions would be really appreciate.

Here below the input for the Pd slab calculated with SP:
&CONTROL
    calculation   = "relax"
    prefix ='Pd_Surface_111_testSP'
    forc_conv_thr =  1.0e-03
    max_seconds   =  1.34369e+14
    nstep         = 400
    pseudo_dir    = "/home/pcosta/pseudo"
verbosity     ='high'
    disk_io ='none'
    tprnfor       = .TRUE.
    tstress       = .TRUE.
/

&SYSTEM
    a     =  1.11278e+01
    b     =  1.66917e+01
    c     =  2.45429e+01
    cosab = -5.00000e-01
    degauss                   =  1.00000e-02
    ecutrho                   =  1.33000e+02
    ecutwfc                   =  3.2000e+01
    lda_plus_u                = .FALSE.
nspin                     = 2
    ibrav = 12
    nat   = 72
    ntyp  = 1
    vdw_corr                  = 'grimme-d3'
    occupations               = "smearing"
    smearing                  = "gaussian"
    starting_magnetization(1) = 2.00000e-01
/

&ELECTRONS
    conv_thr         =  1.00000e-06
    diagonalization  = "david"
    mixing_beta      = 0.2
    electron_maxstep = 450
    startingpot      = "atomic"
    startingwfc      = "atomic+random"
/

&IONS
    ion_dynamics = "bfgs"
/

K_POINTS {gamma}

ATOMIC_SPECIES
Pd    106.42000  Pd.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS {angstrom}
Pd      1.390977   0.803081  14.542918
Pd      4.172936   0.803081  14.542918
Pd     -0.000000   3.212326  14.542915
Pd      2.781956   3.212328  14.542918
Pd     -0.000000   1.606165  12.271460
Pd      2.781956   1.606163  12.271458
Pd     -1.390977   4.015407  12.271460
Pd      1.390977   4.015407  12.271460
Pd      0.000000   0.000000  10.000000
Pd      2.781956   0.000002  10.000002
Pd      1.390979   2.409244  10.000002
Pd      4.172933   2.409244  10.000002
Pd     -1.390979   5.621570  14.542918
Pd      1.390979   5.621570  14.542918
Pd     -2.781956   8.030815  14.542915
Pd      0.000000   8.030817  14.542918
Pd     -2.781956   6.424654  12.271460
Pd      0.000000   6.424652  12.271458
Pd     -4.172933   8.833896  12.271460
Pd     -1.390979   8.833896  12.271460
Pd     -2.781956   4.818489  10.000000
Pd      0.000000   4.818491  10.000002
Pd     -1.390977   7.227733  10.000002
Pd      1.390977   7.227733  10.000002
Pd     -4.172936  10.440059  14.542918
Pd     -1.390977  10.440059  14.542918
Pd     -5.563912  12.849305  14.542915
Pd     -2.781956  12.849306  14.542918
Pd     -5.563912  11.243143  12.271460
Pd     -2.781956  11.243142  12.271458
Pd     -6.954889  13.652385  12.271460
Pd     -4.172936  13.652385  12.271460
Pd     -5.563912   9.636979  10.000000
Pd     -2.781956   9.636980  10.000002
Pd     -4.172933  12.046222  10.000002
Pd     -1.390979  12.046222  10.000002
Pd      6.954889   0.803081  14.542918
Pd      9.736848   0.803081  14.542918
Pd      5.563912   3.212326  14.542915
Pd      8.345868   3.212328  14.542918
Pd      5.563912   1.606165  12.271460
Pd      8.345868   1.606163  12.271458
Pd      4.172936   4.015407  12.271460
Pd      6.954889   4.015407  12.271460
Pd      5.563912   0.000000  10.000000
Pd      8.345868   0.000002  10.000002
Pd      6.954892   2.409244  10.000002
Pd      9.736845   2.409244  10.000002
Pd      4.172933   5.621570  14.542918
Pd      6.954892   5.621570  14.542918
Pd      2.781956   8.030815  14.542915
Pd      5.563912   8.030817  14.542918
Pd      2.781956   6.424654  12.271460
Pd      5.563912   6.424652  12.271458
Pd      1.390979   8.833896  12.271460
Pd      4.172933   8.833896  12.271460
Pd      2.781956   4.818489  10.000000
Pd      5.563912   4.818491  10.000002
Pd      4.172936   7.227733  10.000002
Pd      6.954889   7.227733  10.000002
Pd      1.390977  10.440059  14.542918
Pd      4.172936  10.440059  14.542918
Pd     -0.000000  12.849305  14.542915
Pd      2.781956  12.849306  14.542918
Pd     -0.000000  11.243143  12.271460
Pd      2.781956  11.243142  12.271458
Pd     -1.390977  13.652385  12.271460
Pd      1.390977  13.652385  12.271460
Pd      0.000000   9.636979  10.000000
Pd      2.781956   9.636980  10.000002
Pd      1.390979  12.046222  10.000002
Pd      4.172933  12.046222  10.000002
-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
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