Many large negative frequencies

From NWChem

Viewed 2278 times, With a total of 6 Posts
Jump to: navigation, search

Clicked A Few Times
Threads 8
Posts 20
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

  1. input for optimization

start NbOH3_SiOH3_Na_n_c1M06-L

geometry
zmat angstroms
o
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


  1. 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



  1. 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
Threads 12
Posts 1676
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
Edited On 10:07:14 AM PST - Fri, Nov 6th 2015 by Edoapra

Clicked A Few Times
Threads 8
Posts 20
Thanks a lot Edoapra

So, you changed the grid and changed convergence
So using xfine grid was causing this issue?

Pansy

Forum Vet
Threads 12
Posts 1676
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
Threads 1
Posts 190
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
Threads 12
Posts 1676
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
Threads 8
Posts 20
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


Forum >> NWChem's corner >> General Topics



Who's here now Members 0 Guests 1 Bots/Crawler 0


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC