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I am trying to run an NEB calculation that reacts a sulfite anion with an organic molecule. I've gotten it to converge, and I've added necessary the fcp_tot_charge_first = -2 and fcp_tot_charge_last = -1 that properly describes my reaction. The problem is, when I view my images after convergence is achieved, I notice that my sulfite ion becomes planar. When I ran a relaxation of a sulfite ion by itself with the specified -2 charge, the proper bond angles and molecule geometry emerged. Is it possible that I can specify where the -2 charge should be in the NEB calculation, as not doing so is obviously changing the appropriate bond angles and molecular geometry of one of my reactants (sulfite)? I attempted to add an intermediate image with the sulfite ion having the correct bond angles, yet that did not seem to remedy the problem. Here is my neb.in file:

BEGIN
BEGIN_PATH_INPUT
&PATH
    restart_mode    = 'from_scratch'
    string_method   = 'neb',
    nstep_path      = 200,
    ds              = 1.D0,
    opt_scheme      = "broyden"
    num_of_images   = 12,
    CI_scheme       = "no-CI",
    path_thr        = 0.05D0,
    fcp_tot_charge_first = -2,
    fcp_tot_charge_last = -1,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
    prefix      = "sulf_pyr"
    outdir      = "./outdir",
    pseudo_dir  = '/home/asmaldo1/SSSP_efficiency_pseudos',
/
&SYSTEM
    ibrav=1, 
    celldm(1)=20,
    nat=23, 
    ntyp=5,
    ecutwfc=75,
    occupations='smearing', smearing='gaussian', degauss=0.01
/
/
&ELECTRONS
/
&IONS
ion_dynamics='bfgs'
/
ATOMIC_SPECIES

S   32.065  s_pbe_v1.4.uspp.F.UPF  
O   15.9994 O.pbe-n-kjpaw_psl.0.1.UPF
N   14.00067 N.pbe-n-radius_5.UPF
C   12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF
H   1.00784 H.pbe-rrkjus_psl.1.0.0.UPF

BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS (angstrom)
N             5.4430785377        1.7388709598        1.8017325574  0 0 0
N             0.3289614849        0.9084068628        1.9029571469  0 0 0
C             1.1551109801        2.0175599479        1.9334074379  0 0 0
C             2.6014797497        1.9132794341        1.8941133327  0 0 0 
C             0.3162014957        3.1308458865        2.0178225750
C            -0.9844138574        1.2892191588        1.9484707855  0 0 0
C            -1.0223373707        2.6719606348        2.0312421523
C             3.4071422906        3.0214129160        1.5645878748  0 0 0
C             3.2854123275        0.7139543433        2.1759191892  0 0 0
C             4.7906579711        2.8834637547        1.5343275433  0 0 0
C             4.6764284281        0.6839234338        2.1157678060  0 0 0
H             0.6490325125       -0.0435864281        1.7865661724  0 0 0
H             0.6474856984        4.1611261888        2.0986954023  
H            -1.7883727949        0.5629873562        1.9114829118  0 0 0
H            -1.9244876623        3.2698513663        2.0975913004  
H             2.9505532128        3.9782513856        1.3119158332  0 0 0
H             2.7498484016       -0.1903558892        2.4712524188  0 0 0
H             5.4165933356        3.7402887070        1.2680800684  0 0 0
H             5.2067358558       -0.2453702355        2.3426749264  0 0 0
S             1.9999000000        1.9655000000        5.6458787300  
O             0.7464242772        2.7015016500        6.0978009930  
O             3.2523415152        2.7030524110        6.0975710775
O             2.0010416235        0.5329724275        6.1586491996

INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (angstrom)
N    5.4430785377    1.7388709598    1.8017325574  0 0 0
N    0.3289614849    0.9084068628    1.9029571469  0 0 0
C    1.1551109801    2.0175599479    1.9334074379  0 0 0
C    2.6014797497    1.9132794341    1.8941133327  0 0 0
C    0.3151839600    3.1370198121    2.0064922322
C   -0.9844138574    1.2892191588    1.9484707855  0 0 0
C   -1.0241973193    2.6759222783    2.0159605353
C    3.4071422906    3.0214129160    1.5645878748  0 0 0
C    3.2854123275    0.7139543433    2.1759191892  0 0 0
C    4.7906579711    2.8834637547    1.5343275433  0 0 0
C    4.6764284281    0.6839234338    2.1157678060  0 0 0
H    0.6490325125   -0.0435864281    1.7865661724  0 0 0
H    0.6445894105    4.1738872449    2.0585128798
H   -1.7883727949    0.5629873562    1.9114829118  0 0 0
H   -1.9290477065    3.2761770453    2.0888452089
H    2.9505532128    3.9782513856    1.3119158332  0 0 0
H    2.7498484016   -0.1903558892    2.4712524188  0 0 0
H    5.4165933356    3.7402887070    1.2680800684  0 0 0
H    5.2067358558   -0.2453702355    2.3426749264  0 0 0
S    1.3358324074    2.7455904515    5.2777650801
O    0.3227834487    3.7250731490    5.8410419878
O    2.7192107334    3.2230323226    5.6035176747
O    1.1077357138    1.3728115853    5.8784609419

LAST_IMAGE
ATOMIC_POSITIONS (angstrom)
N             5.4430785377        1.7388709598        1.8017325574
N             0.3289614849        0.9084068628        1.9029571469
C             1.1551109801        2.0175599479        1.9334074379
C             2.6014797497        1.9132794341        1.8941133327
C             0.2726216237        3.0229152709        2.3225616664
C            -0.9844138574        1.2892191588        1.9484707855
C            -1.0859747524        2.4062056714        2.0936835021
C             3.4071422906        3.0214129160        1.5645878748
C             3.2854123275        0.7139543433        2.1759191892
C             4.7906579711        2.8834637547        1.5343275433
C             4.6764284281        0.6839234338        2.1157678060
H             0.6490325125       -0.0435864281        1.7865661724
H             0.5338472143        3.9258893806        1.7505376117
H            -1.7883727949        0.5629873562        1.9114829118
H            -2.0349740019        2.9223034218        2.1912246258
H             2.9505532128        3.9782513856        1.3119158332
H             2.7498484016       -0.1903558892        2.4712524188
H             5.4165933356        3.7402887070        1.2680800684
H             5.2067358558       -0.2453702355        2.3426749264
S             0.3681529180        3.6917578695        4.0695343450
O            -0.2989527328        5.0390751444        4.0116482000
O             1.8073724479        3.8704000944        4.4271441250
O            -0.3214611330        2.7389105110        4.9356456180
END_POSITIONS
K_POINTS (automatic)
 1 1 1 0 0 0
END_ENGINE_INPUT
END

This is clearly affecting my activation energy, so I need to resolve this. I will also add that besides this problem, I am not having convergence issues. Thank you for the help.

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1
  • $\begingroup$ I think a better audience for this question would be Matter Modeling. I can transfer it there, just leave a flag or notify me with a comment. $\endgroup$ – Martin - マーチン Dec 4 '20 at 23:59

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