yambo-4.2.3 install

[Daniele Varsano]

Dear Joydev,
just run p2y in parallel.
If you have many kpoints, of course it takes time, it is an I/O procedure!
I do not what do you mean by much time, anyway this is done once for all and should be manageable.


Best,
Daniele

[joydev de]

Dear Daniele,

I am doing a calculation of c60 for getting the absorption peak around 40eV. For this i have to converge 2000 bands. Now to do yambo calculation, i have to convert p2y. I have tried by two method-
1. serial
2.parallel.

But i alwaya grt a error message for both method.
For serial, the error-
[joydev@jcbose C_scf.save]$ /home/joydev/yambo-4.0.4-rev.107/bin/p2y


__ __ ______ ____ _____
/\ \ /\ \\ _ \ /"\_/`\/\ _`\ /\ __`\
\ `\`\\/"/ \ \L\ \/\ \ \ \L\ \ \ \/\ \
`\ `\ /" \ \ __ \ \ \__\ \ \ _ <" \ \ \ \
`\ \ \ \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
\ \_\ \ \_\ \_\ \_\\ \_\ \____/\ \_____\
\/_/ \/_/\/_/\/_/ \/_/\/___/ \/_____/


<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies... done
<---> Cell data... done
<---> Atomic data... done
<---> Symmetries...[SI no]......[-I no]...[TR yes]
<---> XC functional...Slater exchange(X)+Perdew & Zunger(C)
<---> EXX fraction... 0.000000
<---> EXX screening... 0.000000
<---> K-points mesh... done
<---> RL vectors... done
<05s> IGK arrays... done
<05s> Energies... done
<05s> :: Electrons : 240.0000
<05s> :: Temperature [ev]: 0.000000
<05s> :: Lattice factors [a.u.]: 40.00000 40.00000 40.00000
<05s> :: K-points : 1
<05s> :: Bands : 2000
<05s> :: Spinor components : 1
<05s> :: Spin polarizations : 1
<05s> :: Spin orbit coupling : no
<05s> :: Symmetries [spatial]: 1
<05s> :: [T-rev]: yes
<05s> :: Max WF components : 502479
<05s> :: RL vectors (WF): 502479
<05s> :: RL vectors (CHARGE): 12084189
<05s> :: XC potential : Slater exchange(X)+Perdew & Zunger(C)
<05s> :: Atomic species : 1
<05s> :: Max atoms/species : 60
<05s> == DB1 (Gvecs and more) ...
<05s> ... Database done
<05s> == DB2 (wavefunctions) ...
<05s> [M 7.488 Gb] Alloc wf_disk ( 7.488)
[ERROR][NetCDF] NetCDF: One or more variable sizes violate format constraints

For parallel, the error-mpirun noticed that process rank 2 with PID 23332 on node node02 exited on signal 9 (Killed).
Please tell me about the error.
I am attaching the nscf.in and nscf.out file.

Regards
Joydev

[Daniele Varsano]

This is because netcdf does not support such large files unless you compile them with large file support. You can fragment your databases by typing p2y -b number of bands.

Are you sure that excitations at 40ev are meaningfull?

Best
Daniele

[joydev de]

According to the literature, there is a peak at 40 eV of c60. For this, I have to access high energy level, almost 3000 bands.

Regards
Joydev

[Daniele Varsano]

Dear Joydev,

I know but this is a resonance, I feat that here volume effects (supercells) will play a role.

Good luck,

Daniele

[joydev de]

Dear Daniele,

When i am increasing the number of reciprocal lattice vector in the yambo input file the peak position of the absorption curve changes. Is there any convergence test over number of reciprocal lattice vector?
Another question: How much reciprocal lattice vector I have to consider?

I am attaching a absorption plot of c60 for different lattice vector. You can see the variation from this plot.

Regards
Joydev

[Daniele Varsano]

Dear Joydev,

I assume you mean the G-vectos of the block of the dielectric matrix (NGsBlkXd).
Yes, of course this is a variable that has to be converged. How many? it is clearly system dependent (it depends on the anysotropy of your system, psuedopotentials, volume of the supercelll....).

I invite you to follow some of the tutorials present in the yambo website in order to familiarize with the code and understand the theory behind,
Best,
Daniele

[joydev de]

Dear Daniele Varsano,

Now am calculating the c60 supercell absorption spectrum. When I am converting the p2y, always I am getting an error message.
The error statement is below. Also I am attaching the nscf file.


[joydev@jcbose C_scf.save]$ ~/yambo-4.0.4-rev.107/bin/p2y


____ ____ ___ .___ ___. .______ ______
\ \ / / / \ | \/ | | _ \ / __ \
\ \/ / / ^ \ | \ / | | |_) | | | | |
\_ _/ / /_\ \ | |\/| | | _ < | | | |
| | / _____ \ | | | | | |_) | | `--" |
|__| /__/ \__\ |__| |__| |______/ \______/



<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies... done
<---> Cell data... done
<---> Atomic data... done
<---> Symmetries...[SI no]......[-I no]...[TR yes]
<---> XC functional...Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
<---> EXX fraction... 0.000000
<---> EXX screening... 0.000000
<---> K-points mesh... done
<---> RL vectors... done
<04s> IGK arrays... done
<04s> Energies... done
<04s> :: Electrons : 480.0000
<04s> :: Temperature [ev]: 0.000000
<04s> :: Lattice factors [a.u.]: 28.34589 28.34589 75.58904
<04s> :: K-points : 1
<04s> :: Bands : 1600
<04s> :: Spinor components : 1
<04s> :: Spin polarizations : 1
<04s> :: Spin orbit coupling : no
<04s> :: Symmetries [spatial]: 1
<04s> :: [T-rev]: yes
<04s> :: Max WF components : 550591
<04s> :: RL vectors (WF): 550591
<04s> :: RL vectors (CHARGE): 12454049
<04s> :: XC potential : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
<04s> :: Atomic species : 1
<04s> :: Max atoms/species : 120
<04s> == DB1 (Gvecs and more) ...
<05s> ... Database done
<05s> == DB2 (wavefunctions) ...
<05s> [M 6.564 Gb] Alloc wf_disk ( 6.564)
[ERROR][NetCDF] NetCDF: One or more variable sizes violate format constraints


Sir, what is the problem? Is there any problem in the nscf input file?

Thanking you.

Regards,
Joydev De

[joydev de]

Sorry. The nscf file is not attached in the previous message.

[Daniele Varsano]

Dear Joydev De,

the nscf it is not attached anyway I think it is not needed.

In my opinion the problem can be that:
1) Too much memory required:

Code: Select all

 [M 6.564 Gb] Alloc wf_disk ( 6.564)

2) Netcdf are not compiled with large file support.

For both the case the solution could be that you add the -b option to the p2y, i.e. you fragment the database with a fixed number of bands.
An example could be:

Code: Select all

p2y -b 200

Yambo should generate 8 files contaning the wfs instead that a single file.

Best,

Daniele