Many large negative frequencies

Clicked A Few Times

8:58:07 AM PST - Mon, Nov 2nd 2015

I am running a simple geometry optimization for a number of molecules and I get many very high imaginary frequencies.

I have tried suggestions like doing 'task dft freq numerical' as well but I still get the same large number of imaginary frequencies. I tried different forms of input geometry: xyz coordinates with and without noautoz, zmat format but they all give similar output for frequencies.

Here I am attaching the input file with zmat geometry
and also the output from the frequency calculations

input for optimization

start NbOH3_SiOH3_Na_n_c1M06-L

geometry
zmat angstroms

nb 1 nbo2

o    2 onb3        1 onbo3

o    2 onb4        3 onbo4         1 dih4

si 4 sio5 2 sionb5 3 dih5

o    5 osi6        4 osio6         2 dih6

o    2 onb7        4 onbo7         5 dih7

o    2 onb8        4 onbo8         5 dih8

o    5 osi9        2 osinb9        1 dih9

h    8 ho10        2 honb10        1 dih10

h    3 ho11        2 honb11        1 dih11

h    9 ho12        5 hosi12        2 dih12

h    7 ho13        2 honb13        1 dih13

h    6 ho14        5 hosi14        2 dih14

na 1 nao15 2 naonb15 4 dih15
variables
nbo2 1.995054
onb3 1.931611
onbo3 99.430
onb4 1.998377
onbo4 118.308
dih4 -99.272
sio5 1.650478
sionb5 106.135
dih5 157.850
osi6 1.651175
osio6 116.035
dih6 145.061
onb7 2.547994
onbo7 65.223
dih7 -20.730
onb8 1.933744
onbo8 108.137
dih8 -89.092
osi9 1.660080
osinb9 107.621
dih9 -12.511
ho10 0.962297
honb10 122.176
dih10 -180.000
ho11 0.961802
honb11 127.368
dih11 180.000
ho12 0.968910
hosi12 109.399
dih12 0.991
ho13 0.961256
honb13 122.864
dih13 35.503
ho14 0.960363
hosi14 113.921
dih14 157.534
nao15 0.960674
naonb15 123.579
dih15 -180.000
end
end

basis spherical
O library aug-cc-pvdz
H library aug-cc-pvdz
Si library aug-cc-pvdz
Na library aug-cc-pvdz
Nb library LANL2DZ_ECP
end

ecp
Nb library LANL2DZ_ECP
end

driver
maxiter 500
end

dft
XC M06-L
maxiter 500
grid xfine nodisk
mult 2
end

task dft optimize

input for frequency:

start NbOH3_SiOH3_Na_n_c1_freqM06-L

geometry
o -1.53818182 1.66045046 -1.06002635
nb -0.09296080 0.79146972 -0.45379073
o 0.48976383 2.37543521 0.81035634
o -0.25640017 -0.59787257 1.14433264
si -0.14219494 -2.00822934 0.35615132
o 1.23631740 -2.93021375 0.46511435
o -0.09474250 -1.36466582 -1.25244096
o 1.58416873 0.96308517 -1.54213781
o -1.39763583 -3.08430971 0.55842462
h 2.22591749 1.60330438 -1.21649499
h 0.57626745 2.09567663 1.72584033
h -2.22555113 -2.66871873 0.81107060
h 0.62679400 -1.64730735 -1.82436360
h 1.10101718 -3.78066689 0.88904771
na -1.15209656 3.57930854 -0.06139465
end

basis spherical
O library aug-cc-pvdz
H library aug-cc-pvdz
Si library aug-cc-pvdz
Na library aug-cc-pvdz
Nb library LANL2DZ_ECP
end

ecp
Nb library LANL2DZ_ECP
end

driver
maxiter 500
end

dft
XC M06-L
maxiter 500
grid xfine nodisk
mult 2
end

task dft freq

Here is the Projected modes from the frequency output:

----------------------------------------------------------------------------

Normal Eigenvalue ||           Projected Infra Red Intensities

 Mode   [cm**-1]  || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]

------ ---------- || -------------- ----------------- ---------- -----------

   1   ********** ||    0.117015           2.700       114.072      16.618

   2   ********** ||    0.064080           1.478        62.468       9.100

   3   ********** ||    0.011510           0.266        11.221       1.635

   4   -33687.540 ||    0.078797           1.818        76.816      11.190

   5   -25757.006 ||    0.082701           1.908        80.621      11.744

   6   -23790.050 ||    0.001433           0.033         1.397       0.203

   7   -20757.733 ||    0.010053           0.232         9.800       1.428

   8   -17439.946 ||    0.074213           1.712        72.346      10.539

   9   -15284.915 ||    0.268946           6.205       262.182      38.194

  10   -13926.130 ||    0.043632           1.007        42.534       6.196

  11   -12473.952 ||    0.214737           4.954       209.336      30.495

  12   -11380.426 ||    0.033290           0.768        32.453       4.728

  13   -10635.261 ||    0.026788           0.618        26.114       3.804

  14    -7293.585 ||    0.115221           2.658       112.323      16.363

  15    -6430.577 ||    0.016996           0.392        16.568       2.414

  16    -5972.534 ||    0.050965           1.176        49.683       7.238

  17    -5823.831 ||    0.039314           0.907        38.325       5.583

  18    -4934.130 ||    0.027137           0.626        26.454       3.854

  19    -4557.766 ||    0.078088           1.802        76.124      11.089

  20    -3799.075 ||    0.020188           0.466        19.680       2.867

  21    -3368.273 ||    0.084462           1.949        82.337      11.995

  22    -2947.866 ||    0.076159           1.757        74.244      10.816

  23     1665.733 ||    0.040800           0.941        39.774       5.794

  24     1732.729 ||    0.049395           1.140        48.153       7.015

  25     3763.139 ||    0.047393           1.093        46.201       6.730

  26     3953.995 ||    0.049117           1.133        47.882       6.975

  27     4232.383 ||    0.084387           1.947        82.265      11.984

  28     4415.838 ||    0.051528           1.189        50.232       7.318

  29     4923.068 ||    0.056963           1.314        55.531       8.090

  30     5951.903 ||    0.076721           1.770        74.791      10.895

  31     6826.743 ||    0.038443           0.887        37.476       5.459

  32     7465.567 ||    0.085075           1.963        82.936      12.082

  33     8736.876 ||    0.079897           1.843        77.888      11.346

  34     8753.017 ||    0.143754           3.317       140.139      20.415

  35     9488.011 ||    0.025483           0.588        24.842       3.619

  36    14674.162 ||    0.202052           4.661       196.970      28.694

  37    18461.318 ||    0.029159           0.673        28.425       4.141

  38    21466.692 ||    0.047052           1.086        45.869       6.682

  39    27067.458 ||    0.066196           1.527        64.531       9.401

  40    27289.816 ||    0.036171           0.835        35.262       5.137

  41    31374.369 ||    0.130001           2.999       126.731      18.462

  42    53561.484 ||    0.045293           1.045        44.154       6.432

  43   ********** ||    0.026435           0.610        25.770       3.754

  44   ********** ||    0.124707           2.877       121.571      17.710

  45   ********** ||    0.096995           2.238        94.556      13.774

----------------------------------------------------------------------------

I have tried the same calculation with "task dft freq numerical"
but still get the same result

Any suggestions are welcome, Please

Thanks,

Pansy

Forum Vet

10:27:06 AM PST - Tue, Nov 3rd 2015

These are the frequencies I just got running NWChem 6.6 on a slightly modified input file


 Normal Eigenvalue ||           Projected Infra Red Intensities
  Mode   [cm**-1]  || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]
 ------ ---------- || -------------- ----------------- ---------- -----------
    1       -0.000 ||    0.000097           0.002         0.095       0.014
    2       -0.000 ||    0.000201           0.005         0.196       0.028
    3        0.000 ||    0.002064           0.048         2.012       0.290
    4        0.000 ||    0.001175           0.027         1.145       0.165
    5        0.000 ||    0.001426           0.033         1.391       0.201
    6        0.000 ||    0.000391           0.009         0.381       0.055
    7       37.102 ||    0.007832           0.181         7.635       1.102
    8       48.020 ||    0.003671           0.085         3.579       0.516
    9       66.766 ||    0.005664           0.131         5.521       0.797
   10       92.666 ||    0.004570           0.105         4.455       0.643
   11       99.916 ||    0.015438           0.356        15.050       2.172
   12      141.665 ||    0.011799           0.272        11.503       1.660
   13      144.708 ||    0.062446           1.441        60.876       8.784
   14      175.931 ||    0.029784           0.687        29.035       4.189
   15      211.790 ||    0.014689           0.339        14.320       2.066
   16      236.120 ||    0.007759           0.179         7.564       1.091
   17      252.995 ||    0.007173           0.165         6.993       1.009
   18      263.861 ||    0.003710           0.086         3.616       0.522
...

Here is the input file


start NbOH3_SiOH3_Na_n_c1_freqM06-L

geometry
o    -1.53818182   1.66045046  -1.06002635
nb   -0.09296080   0.79146972  -0.45379073
o     0.48976383   2.37543521   0.81035634
o    -0.25640017  -0.59787257   1.14433264
si   -0.14219494  -2.00822934   0.35615132
o     1.23631740  -2.93021375   0.46511435
o    -0.09474250  -1.36466582  -1.25244096
o     1.58416873   0.96308517  -1.54213781
o    -1.39763583  -3.08430971   0.55842462
h     2.22591749   1.60330438  -1.21649499
h     0.57626745   2.09567663   1.72584033
h    -2.22555113  -2.66871873   0.81107060
h     0.62679400  -1.64730735  -1.82436360
h     1.10101718  -3.78066689   0.88904771
na   -1.15209656   3.57930854  -0.06139465
end

basis spherical
O library aug-cc-pvdz
H library aug-cc-pvdz
Si library aug-cc-pvdz
Na library aug-cc-pvdz
Nb library LANL2DZ_ECP
end

ecp
Nb library LANL2DZ_ECP
end

driver
maxiter 500
end

dft
XC M06-L
maxiter 500
grid fine
convergence energy 1d-8
mult 2
end

task dft optimize
task dft freq

Clicked A Few Times

8:54:30 AM PST - Thu, Nov 5th 2015
Thanks a lot Edoapra So, you changed the grid and changed convergence So using xfine grid was causing this issue? Pansy

Forum Vet

6:07:09 PM PST - Thu, Nov 5th 2015
Quote:Pdpatel Nov 5th 7:54 am Thanks a lot Edoapra So, you changed the grid and changed convergence So using xfine grid was causing this issue? Pansy The source code of M06-L was patched during the NWChem 6.6 development to address some numerical issues. Those fixes might have played a part

Forum Regular

9:07:55 AM PST - Fri, Nov 6th 2015
I think your main problem is that the geometry you specified for the frequency calculation is not at a minimum (or any stationary point), at least according to the test calculation I ran. Edo's input included an optimization before the frequency calculation so even though he specified the same geometry, it was optimized before doing the frequency calculation. As a side note, as the documentation states, analytical second derivatives of the Minnesota functionals are not implemented so any frequency calculation with them will be numerical (i.e. in this case task dft freq and task dft freq numerical will do the exact same calculation).

Forum Vet

10:57:41 AM PST - Fri, Nov 6th 2015
Quote:Sean Nov 6th 8:07 am I think your main problem is that the geometry you specified for the frequency calculation is not at a minimum (or any stationary point), at least according to the test calculation I ran. Edo's input included an optimization before the frequency calculation so even though he specified the same geometry, it was optimized before doing the frequency calculation. Sean is quite right. The fact that I re-optimized the geometry (and using a tighter energy convergence of 1e-8) ensured that we were getting to an absolute miniumum.

Clicked A Few Times

10:05:11 AM PST - Mon, Nov 9th 2015
Quote:Edoapra Nov 6th 9:57 am Quote:Sean Nov 6th 8:07 am I think your main problem is that the geometry you specified for the frequency calculation is not at a minimum (or any stationary point), at least according to the test calculation I ran. Edo's input included an optimization before the frequency calculation so even though he specified the same geometry, it was optimized before doing the frequency calculation. Sean is quite right. The fact that I re-optimized the geometry (and using a tighter energy convergence of 1e-8) ensured that we were getting to an absolute miniumum. Point taken Thanks a lot I redid the same calculation as suggested on 6.5 version But used convergence of 1d-10, which helped (convergence of 1d-8 still gave me two large negative frequencies) Thanks again Pansy

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