Sources of vdw pseudopotentials

Asked by Tony on 2017-03-16

Can anyone share some well tested vdw pseudopotentials for atoms such as H, C, Si,...?
Thank you in advance.

Question information

Language:
English Edit question
Status:
Solved
For:
Siesta Edit question
Assignee:
No assignee Edit question
Solved by:
Tony
Solved:
2017-04-05
Last query:
2017-04-05
Last reply:

This question was reopened

  • 2017-03-17 by Tony
Tony (tony2017) said : #1

Well, I handled myself with Atom

Tony (tony2017) said : #2

When I generated vdw pseudo-potential for C atom, I observed in the OUT file some warning such as:

n = 1 l = 0 s = 0.0
        a extr 1.730
        r extr 0.174
        r zero
        r 90/99 % 0.488 0.795

 n = 2 l = 0 s = 0.0
        a extr 0.352 -0.823
        r extr 0.138 1.208
        r zero 0.377
        r 90/99 % 2.511 3.841

 n = 2 l = 1 s = 0.0
        a extr 0.710
        r extr 1.194
        r zero
        r 90/99 % 3.144 5.250

 n = 3 l = 2 s = 0.0
        a extr 0.205
        r extr 111.620
        r zero
        r 90/99 % 118.006 119.491
        WARNING: This orbital is not bound!

 n = 4 l = 3 s = 0.0
        a extr 0.223
        r extr 111.595
        r zero
        r 90/99 % 118.006 119.491
        WARNING: This orbital is not bound!

I got similar warnings when generating the GGA pseudo-potential. I ran an example for Si in the directory "Tutorial/PS_Generation" of Atom, I also observed such warning in the OUT file.

Do I have to worry bout this?

Tony (tony2017) said : #3

An other question, I have seen that some in put files with prefix "pe", that is not "pg"-pseudopotential generation. What does "pe" stand for? I compared the OUT files generated by these two prefixes they result in different total energies.

Tony (tony2017) said : #4

I am reporting another issue: vdw pseudopotentials do not work with transiesta:

I used the generated vdw pseudopotentials for C and H atoms to make a test with transiesta (calculated for bilayer graphene ribbons). it has showed an error:

GHOST: No ghost state for L = 0
GHOST: WARNING: Ghost state for L = 1
KBgen: WARNING: Ghost states have been detected
KBgen: WARNING: Some parameter should be changed in the
KBgen: WARNING: pseudopotential generation procedure.
Stopping Program from Node: 0
Stopping Program from Node: 0

and calculations stopped.

It is worth noting that I cheched that vdw of C atoms using with Siesta calculation can lead to the band structure of bilayer graphene without any problems. And I noted that there were no Ghost states found in Siesta calculations:

GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2

So why does transiesta report this kind of error?

Tony (tony2017) said : #7

Since no ones has suggested solution for this problem, I had to investigated myself.

Checking in detail I have seen that the error of Ghost state detected comes from the pseudopotential of H atoms, not C atoms. Thus my previous comparison with calculations using C atoms is not relevant.

I did a search and found a topic reported the same issue: https://<email address hidden>/msg06022.html

Although this topic did not show a completed solution, I have eventually figured out the way:

1. Generating a new vdw PP for H atoms with some modification in the inp file:
the input *.inp file of H atoms that I downloaded from the Siesta site has the cutoff radii for different shells in values:
1.33000 1.33000 0.37000 1.33000

Since the PP of C atoms did not show any problem, I tried to learn the setup in *.inp file for C atom and I have observed that the 4h radius should be larger than the others. So I set up a modification in the *.inp of H atom, for instance:
 1.33000 1.33000 0.37000 1.700000
Then I generated again the vdw PP with Atom program.

2. In the main fdf file, I also set (without this setup we still see the error):

%block PS.lmax
   C.vdw 3
   H.vdw 3
%endblock PS.lmax

Combining these 2 solutions, I have successfully removed the error of Ghost state detected.

Hope this information is useful for who has the same issue.

Yelda Kadioglu (yelda) said : #8

Hi, i generated relativistic PP and tried to do SOC calculation with siesta-4.1b3 version but i got an error about ghost state for l=0, i tried block PS.lmax as yours but it didnt solve the problem. I tried to change radius but i dont know what number i write to relevant part. How do you you decide on ? thanks
Yelda