Error in Two times Green function reconstruction

Questions and doubts about features of real-time Yambo (yamb_rt)

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Bo Peng
Posts: 13
Joined: Tue Feb 04, 2020 5:47 pm

Error in Two times Green function reconstruction

Post by Bo Peng » Mon Jun 17, 2024 7:36 pm

Dear Yambo developing team,

I am trying to run real time dynamics to get the retarted Green's function:
I used

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ypp_rt -n g
to construct the two times Green function and then run

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ypp_rt
However, I got the error message below:

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 [07] Two times Green function reconstruction
 ============================================


 [ERROR] STOP signal received while in[07] Two times Green function reconstruction

 [ERROR] Reading File ./HARTREE//ndb.RT_G_lesser_K_section; Variable RT_TIMEs_NOW; NetCDF: Variable not found
 
I am not sure whether this is something wrong with the NetCDF or not. I attached the input and output files below:
https://www.dropbox.com/scl/fi/u4webl6x ... rrj7l&dl=0
You can find them in
3-yambo/FixSymm/HARTREE
I will also try to use my Yambo in another cluster to check whether I could reproduce the error message, and the error message remained there unfortunately...

Thank you in advance!

Best wishes,
Bo
Dr Bo Peng
Nevile Research Fellow, Magdalene College
Theory of Condensed Matter Group, Cavendish Laboratory
University of Cambridge

https://www.tcm.phy.cam.ac.uk/profiles/bp432
https://www.magd.cam.ac.uk/user/peng

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Davide Sangalli
Posts: 617
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Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
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Re: Error in Two times Green function reconstruction

Post by Davide Sangalli » Thu Jun 20, 2024 10:50 am

Dear Bo,

in ypp_rt it is coded is the reconstruction of the two-times "lesser" green function withing GKBA (see GKBA equations). This needs, as input, the time history of the density matrix, called "one time Glesser" in the yambo code.
The latter is generated and written to disk with a real-time propagation with yambo_rt using the proper keyword in the input file

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SaveGhistory
Keep in mind that the file containing the "one time Glesser" history is going to easily become rather large. You may want to control how often you write to disk the "one time Glesser" via the variable (second number)

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% IOtime
 0.5 |0.1 |0.5 |  fs    # [RT] Time between to consecutive I/O (J,P,OCCs - GF - OUTPUT)
%
An example, to reconstruct the two time Glesser at the TD-HSEX level, is provided by these 3 input files:
https://github.com/yambo-code/yambo-tes ... 3_coll_SEX
https://github.com/yambo-code/yambo-tes ... /15_td_sex
https://github.com/yambo-code/yambo-tes ... p_G_lesser

1) First step: generation of the "real-time collisions", equivalent to the BSE kernel. You can add the CVONLY flag to simplify the run

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 HXC_Potential= "HARTREE+SEX CVONLY"          # [SC] SC Potential
2) Second step: real time propagation at the TD-HSEX level (again, add CVONLY if you did so in step 1
3) Generate the two times Green function.
The final output is in this folder: https://github.com/yambo-code/yambo-tes ... /REFERENCE
(look for files with name containing 16_ypp_G_lesser)

An example of the output is provided in this paper (figure 4): https://doi.org/10.1103/PhysRevMaterials.5.083803

If you need the retarded one, you can replace BuildGles with use the input flag

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BuildGret
in step 3.

Please, keep in mind that this is a very advanced feature of the code.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

Bo Peng
Posts: 13
Joined: Tue Feb 04, 2020 5:47 pm

Re: Error in Two times Green function reconstruction

Post by Bo Peng » Thu Jun 20, 2024 7:49 pm

Ciao Davide,

Thank you for the swift response and for the detailed instructions!

I tried to follow the three steps but got some error message in my second step:

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



 <---> [01] MPI/OPENMP structure, Files & I/O Directories
 <---> [02] CORE Variables Setup
 <---> [02.01] Unit cells
 <---> [02.02] Symmetries
 <---> [02.03] Reciprocal space
 <---> [02.04] K-grid lattice
 <---> Grid dimensions      :   6   6   2
 <---> [02.05] Energies & Occupations
 <---> [WARNING] [X] Metallic system
 <---> [03] Transferred momenta grid and indexing
 <---> [04] Dipoles
 <---> [WARNING] Cannot use DIP_P on the flight at the moment. Setting io_DIP=.true.
 <---> [WARNING] Only CV components included
 <---> [05] HARTREE+SEX CVONLY Real-Time Dynamics
 <---> [05.01] Pre-Initialization
 <---> [WARNING] User defined bands (7-10) do not respect level degeneracy
 <---> [05.02] Dipoles

[ERROR] STOP signal received while in[05.02] Dipoles
[ERROR] Reading File ./GKBA//ndb.dipoles_fragment_1; Variable P_square_k_0001_spin_0001; NetCDF: Variable not found
I attached the input files of the two steps below:

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#                                                           
#   __   __     _        __  __       ____      U  ___  u   
#   \ \ / / U  /"\  U u |" \/ "| u U | __") u    \/"_ \/    
#    \ V /   \/ _ \/   \| |\/| |/   \|  _ \/     | | | |    
#   U_|"|_u  / ___ \    | |  | |     | |_) | .-,_| |_| |    
#     |_|   /_/   \_\   |_|  |_|     |____/   \_)-\___/     
# .-,//|(_   \\    >>  <<,-,,-.     _|| \\_        \\       
#  \_) (__) (__)  (__)  (./  \.)   (__) (__)      (__)      
#                                                           
#                                                           
#               Version 4.0.2 Revision 5425                 
#                        MPI Build                          
#                http://www.yambo-code.org                  
#
collisions                   # [R] Eval the extended Collisions
em1s                         # [R Xs] Static Inverse Dielectric Matrix
Chimod= "hartree"            # [X] IP/Hartree/ALDA/LRC/BSfxc
% BndsRnXs
  1 |  16 |                   # [Xs] Polarization function bands
%
NGsBlkXs=  10          Ry    # [Xs] Response block size
% DmRngeXs
  0.10000 |  0.10000 | eV    # [Xs] Damping range
%
% LongDrXs
 0.000000 | 1.000000 | 0.000000 |        # [Xs] [cc] Electric Field
%
# OLD
#Potential= "COHSEX"          # [SC] SC Potential
# NEW
HXC_Potential= "HARTREE+SEX CVONLY"          # [SC] SC Potential
% COLLBands
  7 |  10 |                   # [COLL] Bands for the collisions
%
and

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#  __  __   ________   ___ __ __    _______   ______        
# /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\       
# \ \ \ \ \\::: _  \ \\::\| \| \ \\::: _  \ \\:::_ \ \      
#  \:\_\ \ \\::(_)  \ \\:.      \ \\::(_)  \/_\:\ \ \ \     
#   \::::_\/ \:: __  \ \\:.\-/\  \ \\::  _  \ \\:\ \ \ \    
#     \::\ \  \:.\ \  \ \\. \  \  \ \\::(_)  \ \\:\_\ \ \   
#      \__\/   \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/   
#                                                           
#               Version 3.4.0 Revision 2811                 
#                http://www.yambo-code.org                  
#
negf                         # [R] Real-Time dynamics
ElecTemp=0 K                 #
Gauge= "length"               # [Xd,RT] Gauge type (length|velocity)
% RTBands
  7 |  10 |                   # [RT] Bands
%
RTEvalEnergy
RTEvalEntropy

#
# G ret
#
#GrKind= "HS"                 # [RT] G-ret kind: Lorentzian (QP)/ Hyperbolic secant (HS)
#TwoAlpha= 1                  # [RT] C_nk ~ alpha*Gamma_nk^2
#GfnQP_Wv_E=-1.2000   eV      # [EXTQP G] W Energy reference  (valence)
#% GfnQP_Wv
#  0.300 |  0.0000 |  0.010 | # [EXTQP G] W parameters  (valence) eV|adim|eV^-1
#%
#GfnQP_Wc_E= 1.200   eV       # [EXTQP G] W Energy reference  (conduction)
#% GfnQP_Wc
#  0.300 |  0.0000 |  0.010 | # [EXTQP G] W parameters  (conduction) eV|adim|eV^-1
#%

# HARRLvcs= 339        RL    # [XX] HARTREE  RL components
# EXXRLvcs= 59         RL    # [XX] Exchange RL components
# CORRLvcs= 59         RL    # [XX] Exchange RL components

#
# RT Parameters
#
Integrator= "INV HEUN"    # [RT] Integrator ( "RK2 / EULER" "EXP" "RWA" )
NETime=   2.00000      ps   # [RT] Simulation Time (alternative to NEsteps)
RTstep=   10           as    # [RT] Real Time step length
#LifeInterpKIND= "NONE"               # [RT] Step distribution mode
#% LifeInterpSteps
#  1.500 |  0.500 | fs    # [RT] Step length between and inside two consecutive groups of lifetimes
#%
#RTskipImposeN

#
# ELEL CORR
#
# OLD
#Potential= "COHSEX"          # [SC] SC Potential
# NEW
HXC_Potential= "HARTREE+SEX CVONLY"          # [SC] SC Potential

#
# ELEL SCATT
#


#
# ELPH SCATT
#
#BoseTemp=0 K                 #
#% ElPhModes
#  1 |  6 |                   # [ELPH] Phonon modes included
#%
#RT_T_evol                   # [RT] Use a complete Time evolution instead of the CCA
#UseDebyeE                   # [RT] Use a single Debye energy for all phonon modes
#UpdtDebyeT                  # [RT] Update Bose Temp assuming phonons are always at equilibrium


#
# External Field (or manual pump)
#

# OLD IO FORMAT
% Probe_Freq
 2.60     | 2.60     | eV    # [RT Probe] Frequency
%
Probe_FrStep= 0.000000 eV    # [RT Probe] Frequency step
Probe_Int= 1.E+4    kWLm2    # [RT Probe] Intensity
Probe_Damp= 10.00000   fs    # [RT Probe] Damping
Probe_Width= 10.00000   fs    # [RT Probe] Damping
Probe_kind= "QSSIN"          # [RT Probe] Kind(SIN|RES|ANTIRES|GAUSS|DELTA|QSSIN)
% Probe_Dir
 0.00     | 1.00     | 0.00     |        # [RT Probe] Versor
%

# NEW IO FORMAT
% Field1_Freq
 2.60     | 2.60     | eV    # [RT Probe] Frequency
%
Field1_FrStep= 0.000000 eV    # [RT Probe] Frequency step
Field1_Int= 1.E+4    kWLm2    # [RT Probe] Intensity
Field1_Damp= 10.00000   fs    # [RT Probe] Damping
Field1_Width= 10.00000   fs    # [RT Probe] Damping
Field1_kind= "QSSIN"          # [RT Probe] Kind(SIN|RES|ANTIRES|GAUSS|DELTA|QSSIN)
Field1_pol= "linear"
% Field1_Dir
 0.00     | 1.00     | 0.00     |        # [RT Probe] Versor
%
Field1_Tstart=  0.5   fs      # [RT Field1] Initial Time


#
# OTHER
#
% IOtime
 0.5 |0.1 |0.5 |  fs    # [RT] Time between to consecutive I/O (J,P,OCCs - GF - OUTPUT)
%
DBsIOoff= "DIP"         # [IO] Space-separated list of DB with NO I/O. DB=(DIP,X,HF,COLLs,J,GF,OCCs,WF,SC)
SaveGhistory
It seems that something was wrong with the dipoles in the database?

Best wishes,
Bo
Dr Bo Peng
Nevile Research Fellow, Magdalene College
Theory of Condensed Matter Group, Cavendish Laboratory
University of Cambridge

https://www.tcm.phy.cam.ac.uk/profiles/bp432
https://www.magd.cam.ac.uk/user/peng

Bo Peng
Posts: 13
Joined: Tue Feb 04, 2020 5:47 pm

Re: Error in Two times Green function reconstruction

Post by Bo Peng » Tue Jun 25, 2024 1:37 pm

It seems to me that I always got the same error message:

Code: Select all

NetCDF: Variable not found
Maybe I should try to compile Yambo without NetCDF enabled?

Thanks,
Bo
Dr Bo Peng
Nevile Research Fellow, Magdalene College
Theory of Condensed Matter Group, Cavendish Laboratory
University of Cambridge

https://www.tcm.phy.cam.ac.uk/profiles/bp432
https://www.magd.cam.ac.uk/user/peng

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Daniele Varsano
Posts: 3930
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Error in Two times Green function reconstruction

Post by Daniele Varsano » Fri Jul 05, 2024 7:26 am

Dear Bo,

NetCDF support is automatically enabled, so the problem needs to be found elsewhere. Unfortunately, I'm not familiar with this part of the code so I cannot help.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

Bo Peng
Posts: 13
Joined: Tue Feb 04, 2020 5:47 pm

Re: Error in Two times Green function reconstruction

Post by Bo Peng » Mon Jul 15, 2024 11:09 pm

Ciao Daniele,

Thank you for the clarification! No worries at all. I will just wait.

Best wishes,
Bo

P.S. Sorry for the extremely delay in running the calculations we discussed - I was struggling with computational resources but now the situation got much better. I will try to update you soon.
Dr Bo Peng
Nevile Research Fellow, Magdalene College
Theory of Condensed Matter Group, Cavendish Laboratory
University of Cambridge

https://www.tcm.phy.cam.ac.uk/profiles/bp432
https://www.magd.cam.ac.uk/user/peng

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