Yambo Community Forum

Dear all,
I am facing a problem with the compilation of the Yambo code (Yambo.4.4.0). It is connecting to GitHub during the compilation. But, in the server, only intranet connection is allowed. So could not able to connect to GitHub. Is it possible to compile the code without connecting to the GitHub?
Thanks in advance.




Thanks & regards,
Pritam Bhattacharyya,
Ph.D. student,
IIT Bombay,
Mumbai, INDIA.

Dear Pritam,
In order to compile, Yambo needs some external libraries: iotk,netcdf, netcdff, libxc, lapack,blas
plus others that are optional.
The makefile, download them, configure, compile and automatically link.
You can download and compile them separately and then link them in the phase of compilation of Yambo (you need to. indicate the path where they are compiled in the configure command line, type ./configure -h to see the syntax and the options), but this is much more laborious and prone to errors.
Iotk are contained in the QE package, but the others needs to be downloaded.

Best,
Daniele

PS: You can fill your signature in your user profile in order to avoid to type your signature at each post.

Thank you very much for your valuable reply.


Thanks & regards,
Pritam Bhattacharyya,
Ph.D. student,
IIT Bombay,
Mumbai, INDIA.

Dear Daniele,
Thank you very much again. Finally, I have successfully installed the code.




Thanks & regards,
Pritam Bhattacharyya,
Ph.D. student,
IIT Bombay,
Mumbai, INDIA.

Dear Daniele,
Right now, I am trying to run the examples provided in the "Tutirials". I am very much interested to compute the optical absorption. So, I have started with the example of SiH4 molecule. But, I am getting an error (input and only the last portion of the output):


****************************************************************************************
# __ __ _ __ __ ____ U ___ u
# \ \ / / U /"\ U u |" \/ "| u U | __") u \/"_ \/
# \ V / \/ _ \/ \| |\/| |/ \| _ \/ | | | |
# U_|"|_u / ___ \ | | | | | |_) | .-,_| |_| |
# |_| /_/ \_\ |_| |_| |____/ \_)-\___/
# .-,//|(_ \\ >> <<,-,,-. _|| \\_ \\
# \_) (__) (__) (__) (./ \.) (__) (__) (__)
#
# Version 4.0.0 Revision 4280
# MPI+OpenMP Build
# http://www.yambo-code.org
#
optics # [R OPT] Optics
chi # [R CHI] Dyson equation for Chi.
tddft # [R K] Use TDDFT kernel
Chimod= "ALDA" # [X] IP/Hartree/ALDA/LRC/BSfxc
FxcGRLc= 305 RL # [TDDFT] XC-kernel RL size
NGsBlkXd= 305 RL # [Xd] Response block size
% QpntsRXd
1 | 1 | # [Xd] Transferred momenta
%
% BndsRnXd
1 | 40 | # [Xd] Polarization function bands
%
% EnRngeXd
-10.00000 | 20.00000 | eV # [Xd] Energy range
%
% DmRngeXd
0.10000 | 0.10000 | eV # [Xd] Damping range
%
ETStpsXd= 200 # [Xd] Total Energy steps
% LongDrXd
1.000000 | 0.000000 | 0.000000 | # [Xd] [cc] Electric Field
%

**********************************************************************************************

[03] Transferred momenta grid
=============================

[RD./SAVE//ndb.kindx]---------------------------------------
Fragmentation :no
Polarization last K : 1
QP states : 1 1
X grid is uniform :yes
BS scattering :no
COLL scattering :no
- S/N 008826 -------------------------- v.04.04.00 r.00148 -

IBZ Q-points : 1
BZ Q-points : 1

Q [00001] : 0.00 0.00 0.00 (iku) * weight 1.000000

Q [00001] : 0.00 0.00 0.00 (cc ) * weight 1.000000

[04] Optics
===========

[WF-Rho] Performing Wave-Functions I/O from ./SAVE

[FFT-Rho] Mesh size: 45 45 45


[ERROR] STOP signal received while in :[04] Optics

[ERROR] File ./SAVE//ns.wf_fragments_1_1; Variable WF_COMPONENTS_@_SP_POL1_K1_BAND_GRP_1; NetCDF: Variable not found


*************************************************************************************************************




Thanks & regards,
Pritam Bhattacharyya.

Dear Pritam,
this happens because the tutorials you are running are quite old, and in the meantime, the format of the wavefunction has changed.
You can either:
1) Suggested: Run newer tutorials you can find here:
http://www.yambo-code.org/wiki/index.ph ... =Tutorials
http://www.yambo-code.org/wiki/index.php?title=Modules
the wiki is going to be restructured in these days but you should find all you need.

2) Continue with the old tutorials you are running after having converted the wavefunction by using the command
yambo_dir/bin/ypp -w c (not sure of the suffix in the version you are using, type ypp -H for a legend). A new SAVE directory will be created and you can continue by using the generated wavefunctions.

Best,
Daniele

Dear Daniele,
Finally, I am happy that it's working nicely. Thank you very much for your great help. I am using the latest version of Yambo (Yambo-4.4.0). I have seen the Yambo-wiki but would like to practice all the examples to get a better understanding of this code. Because I am going to use this code extensively to study the optical properties of various low dimensional systems. If I face any other difficulty, I will let you know.
Thank you very much again.





Thanks & regards,
Pritam.

Dear Daniele,
I am currently following the tutorials of 2D-hBN which have been provided in the Yambo educational wiki (http://www.yambo-code.org/wiki/index.ph ... al_systems). But in one of the steps, yambo -F yambo_HF_WR.in -J 2D_WR, I am getting the following error in the terminal:
I have checked the SAVE folder where "ns.wf_fragments_1_1" is present. But I don't know why it is showing error. Please have a look at it.



_| _| _|_| _| _| _|_|_| _|_|
_| _| _| _| _|_| _|_| _| _| _| _|
_| _|_|_|_| _| _| _| _|_|_| _| _|
_| _| _| _| _| _| _| _| _|
_| _| _| _| _| _|_|_| _|_|



<---> [01] CPU structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> [02.04] K-grid lattice
<---> [02.05] Energies [ev] & Occupations
<---> [03] Transferred momenta grid
<---> [04] Coloumb potential Random Integration (RIM)
<---> [05] Bare local and non-local Exchange-Correlation
<---> [WF-HF/Rho] Performing Wave-Functions I/O from ./SAVE
<---> [FFT-HF/Rho] Mesh size: 21 21 150

[ERROR] STOP signal received while in :[05] Bare local and non-local Exchange-Correlation
[ERROR] File ./SAVE//ns.wf_fragments_1_1; Variable WF_COMPONENTS_@_SP_POL1_K1_BAND_GRP_1; NetCDF: Variable not found
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0







Thanks,
Pritam

Dear Pritam,
it is possible you need to convert the Wfs also for these databases by using ypp.

Best,
Daniele

Dear Daniele,
Thank you very much for your support. Still, I am following the tutorial of 2D-hBN. I am getting the following error if I run the command: yambo -J 2D_WR_WC -F yambo_BSE.in. This actually belongs to the "Use the truncated coulomb potential in a BSE calculation" section of the tutorial. Kindly have a look at it.

___ __ _____ __ __ _____ _____
| Y || _ || Y || _ \ | _ |
| | ||. | ||. ||. | / |. | |
\_ _/ |. _ ||.\_/ ||. _ \ |. | |
|: | |: | ||: | ||: | \|: | |
|::| |:.|:.||:.|:.||::. /|::. |
`--" `-- --"`-- --"`-----" `-----"


<---> [01] CPU structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> [02.04] K-grid lattice
<---> [02.05] Energies [ev] & Occupations
<---> [03] Transferred momenta grid
<---> [RL indx] Q-grid:User defined / from ndb.kindx.
<---> X indexes |########################################| [100%] --(E) --(X)
<---> SE indexes |########################################| [100%] --(E) --(X)
<---> [04] Coloumb potential Random Integration (RIM)
<---> [05] Coloumb potential CutOff :box z
<---> [05.01] External/Internal QP corrections
<---> [06] Dynamic Dielectric Matrix (PPA)
<---> [07] Response Functions in Transition space
<---> [WARNING] Null BSE kernel block dimension(s) found.

[ERROR] STOP signal received while in :[07] Response Functions in Transition space
[ERROR] The whole BSE hase zero dimension !
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0





Thanks & regards,
Pritam