NWChem Vibrations & Avogadro

Hello Geoff,

This thread is of great interest to me.
Despite your comment, it is actually
quite necessary to be able
to visualize imaginary frequencies
as they correspond to the vibrational
mode that indicates the
reaction coordinate path to the reactant
and products. To this end I find it not
only an inconvenience but something
that will force me to look for other
molecular visualization software if there
is no good workaround. That is not what
I want to do. I think Avogadro is one of
the best options for visualization…
so is there a workaround?

regards,

Matt S.

Hi all

I posted a question at the NWChem forum
(http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id644/Do_I_have_an_imaginary_frequency…html),
and they suggested I get in touch with the Avogadro developers.

In a B3LYP/cc-pvtz frequency calculation, the log file lists:


Normal Eigenvalue || Projected Derivative Dipole Moments (debye/angs)
Mode [cm**-1] || [d/dqX] [d/dqY] [d/dqZ]
------ ---------- || ------------------ ------------------

 1      -32.993 ||       0.001               0.000 -0.009
 2        0.000 ||      -0.001               0.002 0.012
 3        0.000 ||       0.000              -0.023 0.001
 4        0.000 ||       0.000               0.009 0.001
 5        0.000 ||      -0.001              -0.003 0.017
 6        0.000 ||       0.000               0.011 0.001
 7        0.000 ||       0.006               0.000 -0.074
 8       56.848 ||       0.000               0.000 0.000
 9       77.476 ||      -0.030              -0.001 0.393
10      116.618 ||      -0.244              -0.001 -0.019
11      154.375 ||       0.000               0.000 0.000
12      250.918 ||      -0.001               0.387 0.002

When I try to visualize the file in Avogadro, it does not show me this
-32.99 cm-1 imaginary vibration. Is this expected behavior?

Thanks and regards.


Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837
Fax: 979 845 0158

The current default in Avogadro (and Open Babel, which reads the vibrations) is to ignore the 6 lowest degrees of freedom. This removes rotations and translations.

Now, it seems like this might be useful to set as a user-option: “Show Rotations and Translations” since you sometimes wish to see things like imaginary frequencies.

Hope that helps,
-Geoff

On Nov 9, 2012, at 3:18 PM, Andrew Yeung wrote:

Hi all

I posted a question at the NWChem forum
(http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id644/Do_I_have_an_imaginary_frequency…html),
and they suggested I get in touch with the Avogadro developers.

In a B3LYP/cc-pvtz frequency calculation, the log file lists:


Normal Eigenvalue || Projected Derivative Dipole Moments (debye/angs)
Mode [cm**-1] || [d/dqX] [d/dqY] [d/dqZ]
------ ---------- || ------------------ ------------------

1      -32.993 ||       0.001               0.000 -0.009
2        0.000 ||      -0.001               0.002 0.012
3        0.000 ||       0.000              -0.023 0.001
4        0.000 ||       0.000               0.009 0.001
5        0.000 ||      -0.001              -0.003 0.017
6        0.000 ||       0.000               0.011 0.001
7        0.000 ||       0.006               0.000 -0.074
8       56.848 ||       0.000               0.000 0.000
9       77.476 ||      -0.030              -0.001 0.393

10 116.618 || -0.244 -0.001 -0.019
11 154.375 || 0.000 0.000 0.000
12 250.918 || -0.001 0.387 0.002

When I try to visualize the file in Avogadro, it does not show me this
-32.99 cm-1 imaginary vibration. Is this expected behavior?

Thanks and regards.


Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837
Fax: 979 845 0158


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Thanks Geoff.

Is it specific to NWChem’s output? I ask, because Avogadro displays
Gaussian-calculated imaginary modes quite well. I believe that Gaussian
simply doesn’t print the 6 (or 5) rotations and translations.

Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837
Fax: 979 845 0158

On 2012-11-09 2:55 PM, Geoffrey Hutchison wrote:

The current default in Avogadro (and Open Babel, which reads the vibrations) is to ignore the 6 lowest degrees of freedom. This removes rotations and translations.

Now, it seems like this might be useful to set as a user-option: “Show Rotations and Translations” since you sometimes wish to see things like imaginary frequencies.

Hope that helps,
-Geoff

On Nov 9, 2012, at 3:18 PM, Andrew Yeung wrote:

Hi all

I posted a question at the NWChem forum
(http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id644/Do_I_have_an_imaginary_frequency…html),
and they suggested I get in touch with the Avogadro developers.

In a B3LYP/cc-pvtz frequency calculation, the log file lists:


Normal Eigenvalue || Projected Derivative Dipole Moments (debye/angs)
Mode [cm**-1] || [d/dqX] [d/dqY] [d/dqZ]
------ ---------- || ------------------ ------------------

 1      -32.993 ||       0.001               0.000 -0.009
 2        0.000 ||      -0.001               0.002 0.012
 3        0.000 ||       0.000              -0.023 0.001
 4        0.000 ||       0.000               0.009 0.001
 5        0.000 ||      -0.001              -0.003 0.017
 6        0.000 ||       0.000               0.011 0.001
 7        0.000 ||       0.006               0.000 -0.074
 8       56.848 ||       0.000               0.000 0.000
 9       77.476 ||      -0.030              -0.001 0.393
10      116.618 ||      -0.244              -0.001 -0.019
11      154.375 ||       0.000               0.000 0.000
12      250.918 ||      -0.001               0.387 0.002

When I try to visualize the file in Avogadro, it does not show me this
-32.99 cm-1 imaginary vibration. Is this expected behavior?

Thanks and regards.


Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837
Fax: 979 845 0158


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Is it specific to NWChem’s output? I ask, because Avogadro displays
Gaussian-calculated imaginary modes quite well. I believe that Gaussian
simply doesn’t print the 6 (or 5) rotations and translations.

This is not entirely specific to NWChem, since Open Babel performs the same sort of filtering with GAMESS, Q-Chem, and a few other packages. But yes, in my experience, Gaussian internally filters the rotational and translational modes.

If you’re willing to do a minor bit of code surgery or patching, I can provide an updated version of Open Babel that will not remove these modes from NWChem output files.

Hope that helps,
-Geoff

I want to do. I think Avogadro is one of
the best options for visualization…
so is there a workaround?

Sorry for the delayed reply. There could be a workaround, but it depends on whether you’re willing to compile Avogadro (or actually Open Babel + Avogadro) yourself, or what OS you use.

Basically, the NWChem reader in Open Babel would need to be set to read all vibrations. There’s a line in the code:

        for (unsigned int i = 0; i < freq.size(); i++) {
          if (freq[i] > 10.0) {

So if you’re willing to compile yourself, we can definitely fix this quickly.

Hope that helps,
-Geoff