Bound states

[Javier Hernández Rojas]

Dear all,

If you calculate the binding energy of a cluster

and know that this system is very anharmonic,

is it possible to know with NWCHEM if it has bound states ?

Thanks in advance,

Best regards,

Javier

--

Prof. Javier Hernández-Rojas

Director del Instituto Universitario de

Estudios Avanzados en Física Atómica,

Molecular y Fotónica (IUdEA).

Departamento de Física.

Facultad de Ciencias.

Universidad de La Laguna.

38205, La Laguna, Tenerife

SPAIN, Tlf + 34 922 318255

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[Edoardo Aprà]

Could you be more specific about the states you are referring to? Are those the electronic or vibrational states?

[Javier Hernández Rojas]

Vibrational states, i.e. for the electronic ground state, is it possible to know with nwchem if at least one vibrational state will be inside the well? All this knowing that the well is very anharmonic.

Javier

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[Niri Govind]

Hi Javier,

We don't compute the vibronic levels. Typically, the harmonic frequencies are computed after minimizing the geometry.

Another way is to perform an ab initio MD simulation on the ground state, which can bring in some of the anharmonicities. But this is typically done on a ground electronic state or some other reference electronic state.

If you can give us more information, we may be able to share further thoughts on this. 

Best,

Niri Govind

PNNL

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[Javier Hernández Rojas]

Hi Niri,

It is known that the complex H2-He has a binding energy of around 1.36 meV with only one bound state in the electronic ground state. I have reproduced this energy with nwchem but I don't know how many bound states there are. Indeed, taking the value of zpe that gives nwchem, this complex would be unstable. So, this is my doubt when the binding energy of a system is a few meV.

Thanks,

Javier

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[Javier Hernández Rojas]

Dear all,

I'm calculating the single point energy for

CO2-Xe system and I'm finding problems with the

convergence of the energy using the SCF method.

Please find attached the input/output files of NWCHEM.

Thanks in advance,

Javier

 

[Edoardo Aprà]

The def2-tvzpp basis set for Xe  is not an all-electron basis. Instead, it requires ECP. https://nwchemgit.github.io/ECP.html

Here are the changes to the basis set input section you should try (you should remove the extra SCF options, too, since the default options do work for this case).

...

basis spherical
 C library aug-cc-pvtz
 O library aug-cc-pvtz
 Xe library def2-TZVPP
end
ecp
 Xe library def2-ecp
end

 
scf
 singlet
end

...

[Javier Hernández Rojas]

Many thanks Edoardo.

Sincerely,

Javier

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[Javier Hernández Rojas]

Dear all,

I am calculating the normal mode frequencies of the He-(H2+) system in a T

configuration, i.e. the Helium atom is located perpendicular

to the axis of the H2+ molecule. By using the aug-cc-pvtz basis set

and CCSD(T) calculations, I obtain that all frequencies are positive.

But, doing the same calculations with the "aug-cc-pvqz" basis set,

one negative frequency (transition state) appears. Is it possible?

Thanks in advance.

Javier

[Javier Hernández Rojas]

Dear all,

I am trying to calculate the dynamics of a CO2 molecule

using the QMD module but I obtain the following error message:

"inertia tensor could not be inverted  911". 

Any help would be appreciated. Thanks in advance.

Please find attached the input/output files.

Javier

[Edoardo Aprà]

Please add the linear keyword in the qmd input field

https://nwchemgit.github.io/Gaussian-Basis-AIMD.html#linear-flag-for-linear-molecules

[Javier Hernández Rojas]

Many thanks Edoardo.

Javier

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--

Prof. Javier Hernández-Rojas

Director del Instituto Universitario de

Estudios Avanzados en Física Atómica,

Molecular y Fotónica (IUdEA).

Departamento de Física.

Facultad de Ciencias.

Universidad de La Laguna.

38205, La Laguna, Tenerife

SPAIN, Tlf + 34 922 318255

[Javier Hernández Rojas]

Dear all,

I have tried to optimize an aromatic structure with DFT

and I have obtained one negative eigenvalue. I attach the input/output file.

Any help would be very appreciated. Thanks in advance.

Best regards,

Javier

--

Prof. Javier Hernández-Rojas

Director del Instituto Universitario de

Estudios Avanzados en Física Atómica,

Molecular y Fotónica (IUdEA).

Departamento de Física.

Facultad de Ciencias.

Universidad de La Laguna.

38205, La Laguna, Tenerife

SPAIN, Tlf + 34 922 318255

[Edoardo Aprà]

The two attached input files will get you a hessian with no negative eigenvalues.

The first input file aroma1.nw will calculate an hessian with one negative eigenvalue. If you examine the output file of this calculation,

you will find a line

  Geometry after -100.0% step for mode  1; Step length =  0.153 angstroms

I have copied and pasted the geometry corresponding to this displacement in the second input file aroma2.nw

[Javier Hernández Rojas]

Dear Edoardo,

Thanks for the files, but I have used the input file aroma1.nw and it didn't

done. I attach the output file.

Regards,

Javier

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[Edoardo Aprà]

This looks like a truncated output file to me.

It's hard to tell why the calculation stopped without seeing any error message.

[Javier Hernández Rojas]

Dear all,

I have run a RT_TDDFT approach to calculate 

the absorption spectrum of CO2, but when I

try to do the fourier transform of the dipole

moments, using the codes that you provide, I

obtain the following error message:

 error: load: unable to find file -d50
error: called from:
error:   /home/javierh/NWCHEM/CO2/spec/fft1d.m at line 42, column 6
Traceback (most recent call last):
 File "rotate_fft.py", line 50, in <module>
   main()
 File "rotate_fft.py", line 42, in main
   data = parse_stdin ()
 File "rotate_fft.py", line 36, in parse_stdin
   data = [ [ float(v) for v in l ] for l in rawinp]
 File "rotate_fft.py", line 36, in <listcomp>
   data = [ [ float(v) for v in l ] for l in rawinp]
 File "rotate_fft.py", line 36, in <listcomp>
   data = [ [ float(v) for v in l ] for l in rawinp]
ValueError: could not convert string to float: 'GNU'

I used the command:

"octave fft1d.m -d50 -z -p50000 < x.dat | python3.6 rotate_fft.py > xw.dat
"

I attach the output file, "sal" and the x-component of the 

dipole moment "x.dat". Any help would be very appreciated. 

Thanks in advance.

Javier

--

Javier Hernández Rojas

Catedrático de Universidad

Física Atómica, Molecular y Nuclear

Departamento de Física e IUdEA.

Facultad de Ciencias.

38200, La Laguna, Tenerife.

Spain, Tlf +34 922318255

[Edoardo Aprà]

If you read the first 34 lines of the octave script fft1d.m, you can see that what is reported in the NWChem documentation is not entirely accurate.

To be more precise, the fft1d.m script does not have any option. Damping and padding can be turned on by editing the fft1d.m script, instead.

In other words, the command line you reported should be modified as

octave fft1d.m  x.dat | grep -v period | python ./rotate_fft.py > xw.dat

[Javier Hernández Rojas]

Thanks for your help Edoardo. However, I used the new command line and I obtained other error message

associated with the routine "rotate_fft.py", such as:

warning: docstring file '/usr/share/octave/3.8.2/etc/built-in-docstrings' not found

Traceback (most recent call last):

 File "./rotate_fft.py", line 50, in <module>
   main()
 File "./rotate_fft.py", line 42, in main
   data = parse_stdin ()
 File "./rotate_fft.py", line 36, in parse_stdin

   data = [ [ float(v) for v in l ] for l in rawinp]

ValueError: could not convert string to float: GNU

Javier

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[Edoardo Aprà]

The following works for me

wget https://nwchemgit.github.io/RT_TDDFT_scripts.tgz
tar xzf RT_TDDFT_scripts.tgz
cd rt_tddft_scripts
wget https://nwchemgit.github.io/RT_TDDFT_h2o_abs.nwo.gz
gzip -d RT_TDDFT_h2o_abs.nwo
python nw_rtparse.py -xdipole -px -tkick_x RT_TDDFT_h2o_abs.nwo > x.dat

octave fft1d.m  x.dat | grep -v period | python ./rotate_fft.py > xw.dat

[Edoardo Aprà]

$ octave --version

GNU Octave, version 6.4.0
Copyright (C) 2021 The Octave Project Developers.

[Javier Hernández Rojas]

Thanks Eduardo. I had a problem with the octave installation. Now it works.

Javier

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