PDCharges
Gets Around
4:59:43 AM PST - Wed, Feb 8th 2012
Hi,

I am interested in multi-site charge models.
May I setup additional points for the partial charges determination, as well as shift available points from the nuclei?

Forum Vet
10:00:36 AM PST - Wed, Feb 8th 2012
Your question is very cryptic. What kind of calculation are you trying to do?

Bert


Quote:P99 Feb 8th 11:59 am
Hi,

I am interested in multi-site charge models.
May I setup additional points for the partial charges determination, as well as shift available points from the nuclei?

Gets Around
1:14:37 AM PST - Thu, Feb 9th 2012
For example, if I want to make a five-site model of water, then I need to determine the charges not only on the nuclei of atoms, but also on the points representing the lone pair.
In general, the number of charged points does not correspond to the number of nuclei, and the spatial positions does not correspond to the spatial positions of the nuclei.

Forum Vet
6:39:30 PM PST - Thu, Feb 9th 2012
We currently cannot calculate the charge or electron density at an arbitrary point in space. This should not be that hard to do, we have the infrastructure in place to do it, just need to work on getting the coordinates of the points read in.

We will put this on our list for the next release version.

Bert



Quote:P99 Feb 9th 8:14 am
For example, if I want to make a five-site model of water, then I need to determine the charges not only on the nuclei of atoms, but also on the points representing the lone pair.
In general, the number of charged points does not correspond to the number of nuclei, and the spatial positions does not correspond to the spatial positions of the nuclei.

Gets Around
12:30:46 AM PST - Fri, Feb 10th 2012
We do not need to calculate the electron density, or to do anything in the quantum part of the program.
All we need is allow user to specify points for the partial charges, but does not put them on nuclei automatically.

Forum Vet
11:05:37 AM PST - Fri, Feb 10th 2012
Geometry
 bq 1.0 0.5  0.0 charge 0.2

 O  1.1 0.5  0.0

 H  2.1 0.5  0.5

 H  2.1 0.5 -0.5
end

bq is not an atom but a point charge with the charge you can define.

Bert



Quote:P99 Feb 10th 7:30 am
We do not need to calculate the electron density, or to do anything in the quantum part of the program.
All we need is allow user to specify points for the partial charges, but does not put them on nuclei automatically.

Gets Around
8:26:44 AM PST - Mon, Feb 13th 2012
Quote:Bert Feb 10th 6:05 pm
Geometry
 bq 1.0 0.5  0.0 charge 0.2

 O  1.1 0.5  0.0

 H  2.1 0.5  0.5

 H  2.1 0.5 -0.5
end

bq is not an atom but a point charge with the charge you can define.

Bert

Forum Vet
10:34:23 AM PST - Mon, Feb 13th 2012
This should work. Please post the full input deck.

Bert


Quote:P99 Feb 13th 3:26 pm
Quote:Bert Feb 10th 6:05 pm
Geometry
 bq 1.0 0.5  0.0 charge 0.2

 O  1.1 0.5  0.0

 H  2.1 0.5  0.5

 H  2.1 0.5 -0.5
end

bq is not an atom but a point charge with the charge you can define.

Bert

Gets Around
2:54:46 AM PST - Wed, Feb 15th 2012
Quote:Bert Feb 13th 5:34 pm
This should work. Please post the full input deck.

Bert


This one.
It sounds that for MP2 "bq" is a point in the space, but DFT requires an element.

start nw
memory stack 600 mb heap 100 mb global 800 mb
charge 0

geometry 
 O    -0.989 0.6203 0.0827   
 H    -0.3665 1.1207 -0.4459 
 H    -1.6444 1.259 0.3632    
 bq   -0.67775 0.8705 -0.1816
 bq   -1.3167 0.93965 0.22295
end 

basis cartesian
 * library 6-311++G(2d,2p)
end 

dft 
 xc pbe0
end 

esp 
 recalculate 
 probe   0.07
 range   0.3
 factor  1
 spacing 0.02
end 

property 
 dipole 
 quadrupole 
end 

task DFT property
task esp

Forum Vet
5:26:33 PM PST - Wed, Feb 15th 2012
OK, I think I see what you want. You want to have the ESP charges at the coordinates represented by the Bqs. This is not the way this should be done. Bq's are considered to be charges and there is a charge expected to go with it. Without a real charge there the code gets confused. However, there is an alternative: Replace bq with X.

geometry 
O    -0.989 0.6203 0.0827   

H    -0.3665 1.1207 -0.4459 

H    -1.6444 1.259 0.3632    

X    -0.67775 0.8705 -0.1816

X    -1.3167 0.93965 0.22295
end

Bert

Quote:P99 Feb 15th 9:54 am
Quote:Bert Feb 13th 5:34 pm
This should work. Please post the full input deck.

Bert


This one.
It sounds that for MP2 "bq" is a point in the space, but DFT requires an element.

start nw
memory stack 600 mb heap 100 mb global 800 mb
charge 0

geometry 
 O    -0.989 0.6203 0.0827   
 H    -0.3665 1.1207 -0.4459 
 H    -1.6444 1.259 0.3632    
 bq   -0.67775 0.8705 -0.1816
 bq   -1.3167 0.93965 0.22295
end 

basis cartesian
 * library 6-311++G(2d,2p)
end 

dft 
 xc pbe0
end 

esp 
 recalculate 
 probe   0.07
 range   0.3
 factor  1
 spacing 0.02
end 

property 
 dipole 
 quadrupole 
end 

task DFT property
task esp

Gets Around
2:57:19 AM PST - Thu, Feb 16th 2012
Yes, this is what I want.
Unfortunately, the replacement from bq to X leads to crash:

                                 NWChem DFT Module
                                 -----------------


 ------------------------------------------------------------------------
 bas_tag_lib: tag does not refer to an atom        0
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line : 
    34: task DFT property
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 There is an error in the input file
 ------------------------------------------------------------------------


Quote:Bert Feb 16th 12:26 am
OK, I think I see what you want. You want to have the ESP charges at the coordinates represented by the Bqs. This is not the way this should be done. Bq's are considered to be charges and there is a charge expected to go with it. Without a real charge there the code gets confused. However, there is an alternative: Replace bq with X.

geometry 
O    -0.989 0.6203 0.0827   

H    -0.3665 1.1207 -0.4459 

H    -1.6444 1.259 0.3632    

X    -0.67775 0.8705 -0.1816

X    -1.3167 0.93965 0.22295
end

Bert

Forum Vet
2:40:58 PM PST - Thu, Feb 16th 2012
add charge to bq value
You need to add the charge value to the bq line to make it a point charge, e.g.

bq x y z charge 1.

The modified input becomes


start nw

memory stack 600 mb heap 100 mb global 800 mb
charge 0

geometry
O -0.989 0.6203 0.0827
H -0.3665 1.1207 -0.4459
H -1.6444 1.259 0.3632
bq -0.67775 0.8705 -0.1816 charge 1.
bq -1.3167 0.93965 0.22295 charge 1.
end

basis cartesian
* library 6-311++G(2d,2p)
end

dft
xc pbe0
end

esp
recalculate
probe 0.07
range 0.3
factor 1
spacing 0.02
end

property
dipole
quadrupole
end

task DFT property
task esp

Forum Vet
6:54:00 PM PST - Fri, Feb 17th 2012
Sorry, this is another feature we need to address in the code with respect to defining a basis set as *. The following input deck works:

start nw
memory stack 600 mb heap 100 mb global 800 mb
charge 0

geometry 
O    -0.989 0.6203 0.0827   

H    -0.3665 1.1207 -0.4459 

H    -1.6444 1.259 0.3632    

X    -0.67775 0.8705 -0.1816

X    -1.3167 0.93965 0.22295
end

basis cartesian
O library 6-311++G(2d,2p)

H library 6-311++G(2d,2p)
end

dft 
xc pbe0
end

esp 
recalculate 

probe   0.07

range   0.3

factor  1

spacing 0.02
end

property 
dipole 

quadrupole
end

task DFT property
task esp


Bert



Quote:P99 Feb 16th 9:57 am
Yes, this is what I want.
Unfortunately, the replacement from bq to X leads to crash:

                                 NWChem DFT Module
                                 -----------------


 ------------------------------------------------------------------------
 bas_tag_lib: tag does not refer to an atom        0
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line : 
    34: task DFT property
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 There is an error in the input file
 ------------------------------------------------------------------------


Quote:Bert Feb 16th 12:26 am
OK, I think I see what you want. You want to have the ESP charges at the coordinates represented by the Bqs. This is not the way this should be done. Bq's are considered to be charges and there is a charge expected to go with it. Without a real charge there the code gets confused. However, there is an alternative: Replace bq with X.

geometry 
O    -0.989 0.6203 0.0827   

H    -0.3665 1.1207 -0.4459 

H    -1.6444 1.259 0.3632    

X    -0.67775 0.8705 -0.1816

X    -1.3167 0.93965 0.22295
end

Bert


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