Dummy atoms directive in NWChem


Gets Around
Hi,
I'm sorry to previously place the question in General Section, it seems more fit here. Please respond.

I'm using NWChem to calculate DFT energy between 2 monomers. But, what am I supposed to do if I want to replace the 2 monomers with dummy atoms and calculate DFT energy ?

The code I was using to calculate DFT energy between 2 monomers is:

title 'bond_energy'
start dimer
geometry units angstrom
  N 5.286 28.124 48.085 
  H 5.966 28.410 48.528 
  O 7.110 29.056 50.252 
  C 7.758 28.682 51.230
end
basis "ao basis"
  * library 6-311+g*
  bqN library N 6-311+g*
  bqH library H 6-311+g*
  bqO library O 6-311+g*
  bqC library C 6-311+g*
end
dft
  xc m06-2x
  direct
  grid fine
  iterations 10000
end
bsse
  mon first 1 2
  mon second 3 4
end
task dft energy


Here, I'm trying to replace the H with dummy atom, no charge.
So, I wrote the following code:

title 'bond_energy'
start dimer
geometry units angstrom
  N 5.286 28.124 48.085 
  bqH 5.966 28.410 48.528 
  O 7.110 29.056 50.252 
  C 7.758 28.682 51.230
end
basis "ao basis"
  * library 6-311+g*
  bqN library N 6-311+g*
  bqH library H 6-311+g*
  bqO library O 6-311+g*
  bqC library C 6-311+g*
end
dft
 odft
  xc m06-2x
  direct
  grid fine
  mult 2
  iterations 10000
end
bsse
  mon first 1 2
  mult 2
  mon second 3 4 
end
task dft energy


However this gives me an error:
 *********************************
* INPUT ERROR *
* please define bq+element name *
* in the geometry section *
* e.g. bqSi *
*********************************

I think I have mentioned "bqH" then why is this error ?

Is there something wrong with the code ?

Please suggest me a way out.

Thank you.

Forum Vet
This is the input for calculating the interaction energy between the monomers NH and CO

title 'bond_energy'
start dimer
geometry units angstrom
  N 5.286 28.124 48.085
  H 5.966 28.410 48.528
  O 7.110 29.056 50.252
  C 7.758 28.682 51.230
end
basis "ao basis"
  * library 6-311+g*
  bqN library N 6-311+g*
  bqH library H 6-311+g*
  bqO library O 6-311+g*
  bqC library C 6-311+g*
end
dft
 odft
  xc m06-2x
  direct
  grid fine
  iterations 10000
end
bsse
  mon first 1 2
  mon second 3 4
end
task dft energy

Gets Around
Quote:Edoapra May 4th 9:27 am
This is the input for calculating the interaction energy between the monomers NH and CO

title 'bond_energy'
start dimer
geometry units angstrom
  N 5.286 28.124 48.085
  H 5.966 28.410 48.528
  O 7.110 29.056 50.252
  C 7.758 28.682 51.230
end
basis "ao basis"
  * library 6-311+g*
  bqN library N 6-311+g*
  bqH library H 6-311+g*
  bqO library O 6-311+g*
  bqC library C 6-311+g*
end
dft
 odft
  xc m06-2x
  direct
  grid fine
  iterations 10000
end
bsse
  mon first 1 2
  mon second 3 4
end
task dft energy


Yes. That I know. I was not asking that.
I want to calculate the energy using H as a ghost or dummy. What should be the directive for that?

Please answer. I can't find any directive in Nwchem website to solve this.

PS: I have calculated the NH OC interaction energy. Now I want to do the same calculation using H as a dummy/ghost atom to check the deviation of the energy.

Forum Vet
Please explain more in detail what you mean by H as a ghost or dummy.
I don't understand how you can compute BSSE correction on a ghost atom. You can only compute energy. Please let me know me know what I am missing

Gets Around
Yes. Sorry if I'm not clear enough. I do not know how to do it in nwchem.
I have calculated the NH CO interaction energy. (E)
Now I want to declare H atom a dummy and calculate energy of the cluster/group. (Ed)

Will this code help?
title 'bond_energy'
start dimer
geometry units angstrom
  N   45.299 45.201 9.310
  bqH 44.989 45.977 9.108
  O   43.891 47.384 8.180
  C   43.424 48.511 7.918
end
basis "ao basis"
  * library 6-311+g*
  bqN library N 6-311+g*
  bqH library H 6-311+g*
  bqO library O 6-311+g*
  bqC library C 6-311+g*
end
dft
  odft
  xc m06-2x
  direct
  grid medium
  mult 2
  #convergence energy 1e-8
  iterations 5000
end
task dft energy


The energy comes as:

         Total DFT energy =     -167.761723617509
      One electron energy =     -299.695469396600
           Coulomb energy =      116.058018632894
    Exchange-Corr. energy =      -20.428990485658
 Nuclear repulsion energy =       36.304717631855

 Numeric. integr. density =       20.999999626383

     Total iterative time =     10.6s



Is this represent the energy of NCO group where H is a dummy ? I'm unsure about the calculation please comment.

Thank you

Forum Vet
Your first input works, and your last input does produce results, but cannot give supramolecular energy. NWCHEM6.8 precompiled on Ubuntu 17.10.2 can reproduce the results here obtained by itself on MAC.

Gets Around
Error in Nwchem Directive
Why the following code is raising an error ?

title 'bond_energy'
start dimer
geometry units angstrom
  N 5.286 28.124 48.085 
  bqH 5.966 28.410 48.528 
  O 7.110 29.056 50.252 
  C 7.758 28.682 51.230
end
basis "ao basis"
  * library 6-311+g*
  bqN library N 6-311+g*
  bqH library H 6-311+g*
  bqO library O 6-311+g*
  bqC library C 6-311+g*
end
dft
 odft
  xc m06-2x
  direct
  grid fine
  mult 2
  iterations 10000
end
bsse
  mon first 1 2
  mult 2
  mon second 3 4 
end
task dft energy


The Error I'm getting:
*********************************

 * INPUT ERROR                   *

 * please define bq+element name *

 * in the geometry section       *

 * e.g. bqSi                     *

 *********************************
-----------------------------------------------------------------------
  bq DFT atom with no atom type                    0
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line : 
    42: task dft energy




How am I supposed to calculate BSSE energy in presence of DUMMY ATOM ??

A lot of answers are given, but none yet solve my issue with the DIRECTIVE.. !!


Forum >> NWChem's corner >> Running NWChem