BSE result not compatible with ypp input

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BSE result not compatible with ypp input

Postby Yadong Wei » Sat Nov 03, 2018 4:06 pm

Dear Developers:
I used to calculate the BSE optical properties of MoSe2 monolayer and successfully got the output of eps, eel and jdos.
However, when analysing post with ypp I got this message
[root@major1028 3-MSSe]# ypp -J 2D_WR_WC -e s
<---> [01] CPU structure, Files & I/O Directories
<---> CPU-Threads:1(CPU)-24(threads)
<---> [02] Y(ambo) P(ost)/(re) P(rocessor)
<---> [03] Core DB
<---> :: Electrons : 18.00000
<---> :: Temperature [ev]:0.9500E-3
<---> :: Lattice factors [a.u.]: 6.16844 5.34203 32.85081
<---> :: K points : 576
<---> :: Bands : 70
<---> :: Symmetries : 1
<---> :: RL vectors : 68033
<---> [04] K-point grid
<---> :: Q-points (IBZ): 576
<---> :: X K-points (IBZ): 576
<---> [05] CORE Variables Setup
<---> [05.01] Unit cells
<---> [05.02] Symmetries
<---> [WARNING]Spatial Inversion not found among the given symmetry list
<---> [05.03] RL shells
<---> [05.04] K-grid lattice
<---> [05.05] Energies [ev] & Occupations
<---> [06] Excitonic Properties
[ERROR] STOP signal received while in :[06] Excitonic Properties
[ERROR] ndb.BSS_diago, SEC 1, not compatible with ypp input

The BSE input file shows here
Code: Select all
rim_cut                        # [R RIM CUT] Coulomb potential
optics                         # [R OPT] Optics
ppa                            # [R Xp] Plasmon Pole Approximation
bss                            # [R BSS] Bethe Salpeter Equation solver
bse                            # [R BSE] Bethe Salpeter Equation.
bsk                            # [R BSK] Bethe Salpeter Equation kernel
em1d                           # [R Xd] Dynamical Inverse Dielectric Matrix
StdoHash=  40                  # [IO] Live-timing Hashes
Nelectro= 18.00000             # Electrons number
ElecTemp=  0.02587     eV      # Electronic Temperature
BoseTemp=  0.02586     eV      # Bosonic Temperature
OccTresh=0.1000E-4             # Occupation treshold (metallic bands)
NLogCPUs=0                     # [PARALLEL] Live-timing CPU`s (0 for all)
DBsIOoff= "none"               # [IO] Space-separated list of DB with NO I/O. DB=(DIP,X,HF,COLLs,J,GF,CARRIERs,W,SC,BS,ALL)
DBsFRAGpm= "none"              # [IO] Space-separated list of +DB to FRAG and -DB to NOT FRAG. DB=(DIP,X,W,HF,COLLS,K,BS,QINDX,RT,ELP
FFTGvecs= 10797        RL      # [FFT] Plane-waves
WFbuffIO                      # [IO] Wave-functions buffered I/O
PAR_def_mode= "balanced"       # [PARALLEL] Default distribution mode ("balanced"/"memory"/"workload")
X_all_q_CPU= ""                # [PARALLEL] CPUs for each role
X_all_q_ROLEs= ""             # [PARALLEL] CPUs roles (q,g,k,c,v)
X_all_q_nCPU_LinAlg_INV= 1     # [PARALLEL] CPUs for Linear Algebra
X_Threads=0                    # [OPENMP/X] Number of threads for response functions
DIP_Threads=0                  # [OPENMP/X] Number of threads for dipoles
BS_CPU= ""                     # [PARALLEL] CPUs for each role
BS_ROLEs= ""                   # [PARALLEL] CPUs roles (k,eh,t)
BS_nCPU_LinAlg_INV= 1          # [PARALLEL] CPUs for Linear Algebra
BS_nCPU_LinAlg_DIAGO= 1        # [PARALLEL] CPUs for Linear Algebra
K_Threads=0                    # [OPENMP/BSK] Number of threads for response functions
NonPDirs= "none"               # [X/BSS] Non periodic chartesian directions (X,Y,Z,XY...)
RandQpts= 1000000              # [RIM] Number of random q-points in the BZ
RandGvec= 13           RL      # [RIM] Coulomb interaction RS components
#QpgFull                       # [F RIM] Coulomb interaction: Full matrix
% Em1Anys
 0.00     | 0.00     | 0.00     |        # [RIM] X Y Z Static Inverse dielectric matrix
%
IDEm1Ref=0                     # [RIM] Dielectric matrix reference component 1(x)/2(y)/3(z)
CUTGeo= "box z"                # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere X/Y/Z/XY..
% CUTBox
  0.00000 |  0.00000 | 31.50000 |        # [CUT] [au] Box sides
%
CUTRadius= 0.000000            # [CUT] [au] Sphere/Cylinder radius
CUTCylLen= 0.000000            # [CUT] [au] Cylinder length
#CUTCol_test                   # [CUT] Perform a cutoff test in R-space
Chimod= "Hartree"              # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
ChiLinAlgMod= "lin_sys"        # [X] inversion/lin_sys
BSEmod= "retarded"             # [BSE] resonant/retarded/coupling
BSKmod= "SEX"                  # [BSE] IP/Hartree/HF/ALDA/SEX
BSSmod= "d"                    # [BSS] (h)aydock/(d)iagonalization/(i)nversion/(t)ddft`
DbGdQsize= 1.000000            # [X,DbGd][o/o] Percentual of the total DbGd transitions to be used
BSENGexx=  68033       RL      # [BSK] Exchange components
#ALLGexx                       # [BSS] Force the use use all RL vectors for the exchange part
BSENGBlk= 109          RL      # [BSK] Screened interaction block size
#WehDiag                       # [BSK] diagonal (G-space) the eh interaction
#WehCpl                        # [BSK] eh interaction included also in coupling
KfnQPdb= "none"                # [EXTQP BSK BSS] Database
KfnQP_N= 1                     # [EXTQP BSK BSS] Interpolation neighbours
% KfnQP_E
 1.194400 | 1.000000 | 1.000000 |        # [EXTQP BSK BSS] E parameters  (c/v) eV|adim|adim
%
KfnQP_Z= ( 1.000000 , 0.000000 )       # [EXTQP BSK BSS] Z factor  (c/v)
KfnQP_Wv_E= 0.000000   eV      # [EXTQP BSK BSS] W Energy reference  (valence)
% KfnQP_Wv
 0.00     | 0.00     | 0.00     |        # [EXTQP BSK BSS] W parameters  (valence) eV| 1|eV^-1
%
KfnQP_Wv_dos= 0.000000 eV      # [EXTQP BSK BSS] W dos pre-factor  (valence)
KfnQP_Wc_E= 0.000000   eV      # [EXTQP BSK BSS] W Energy reference  (conduction)
% KfnQP_Wc
 0.00     | 0.00     | 0.00     |        # [EXTQP BSK BSS] W parameters  (conduction) eV| 1 |eV^-1
%
KfnQP_Wc_dos= 0.000000 eV      # [EXTQP BSK BSS] W dos pre-factor  (conduction)
DipApproach= "G-space v"       # [Xd] [G-space v/R-space x/Covariant/Shifted grids]
#DipPDirect                    # [Xd] Directly compute <v> also when using other approaches for dipoles
ShiftedPaths= ""               # [Xd] Shifted grids paths (separated by a space)
Gauge= "length"                # [BSE] Gauge (length|velocity)
#NoCondSumRule                 # [BSE] Do not impose the conductivity sum rule in velocity gauge
#MetDamp                       # [BSE] Define \w+=sqrt(\w*(\w+i\eta))
DrudeWBS= ( 0.00     , 0.00     )  eV  # [BSE] Drude plasmon
#Reflectivity                  # [BSS] Compute reflectivity at normal incidence
BoseCut=  0.10000              # [BOSE] Finite T Bose function cutoff
% BEnRange
  0.00000 | 10.00000 | eV      # [BSS] Energy range
%
% BDmRange
  0.05000 |  0.05000 | eV      # [BSS] Damping range
%
BEnSteps=1001                     # [BSS] Energy steps
% BLongDir
 1.000000 | 1.00000 | 0.000000 |        # [BSS] [cc] Electric Field
%
% BSEBands
   17 |  22 |                   # [BSK] Bands range
%
% BSEEhEny
-1.000000 |-1.000000 | eV      # [BSK] Electron-hole energy range
%
WRbsWF                        # [BSS] Write to disk excitonic the WFs
#BSSPertWidth                  # [BSS] Include QPs lifetime in a perturbative way
XfnQPdb= "none"                # [EXTQP Xd] Database
XfnQP_N= 1                     # [EXTQP Xd] Interpolation neighbours
% XfnQP_E
 0.000000 | 1.000000 | 1.000000 |        # [EXTQP Xd] E parameters  (c/v) eV|adim|adim
%
XfnQP_Z= ( 1.000000 , 0.000000 )       # [EXTQP Xd] Z factor  (c/v)
XfnQP_Wv_E= 0.000000   eV      # [EXTQP Xd] W Energy reference  (valence)
% XfnQP_Wv
 0.00     | 0.00     | 0.00     |        # [EXTQP Xd] W parameters  (valence) eV| 1|eV^-1
%
XfnQP_Wv_dos= 0.000000 eV      # [EXTQP Xd] W dos pre-factor  (valence)
XfnQP_Wc_E= 0.000000   eV      # [EXTQP Xd] W Energy reference  (conduction)
% XfnQP_Wc
 0.00     | 0.00     | 0.00     |        # [EXTQP Xd] W parameters  (conduction) eV| 1 |eV^-1
%
XfnQP_Wc_dos= 0.000000 eV      # [EXTQP Xd] W dos pre-factor  (conduction)
% QpntsRXp
    1 |  576 |                 # [Xp] Transferred momenta
%
% BndsRnXp
   1 |  40 |                   # [Xp] Polarization function bands
NGsBlkXp= 109          RL      # [Xp] Response block size
CGrdSpXp= 100.0000             # [Xp] [o/o] Coarse grid controller
% EhEngyXp
-1.000000 |-1.000000 | eV      # [Xp] Electron-hole energy range
%
% LongDrXp
0.7071E-5 |0.7071E-5 | 0.000    |        # [Xp] [cc] Electric Field
%
PPAPntXp= 27.21138     eV      # [Xp] PPA imaginary energy
XTermKind= "none"              # [X] X terminator ("none","BG" Bruneval-Gonze)
XTermEn= 40.00000      eV      # [X] X terminator energy (only for kind="BG")

I opened the WRbsWF and included the spin-orbit coupling using pwscf before solving BSE, and there exists ndb.BS_diago_Q01 in my 2D_WR_WC directory after completing the BSE calculation.
Is there anything wrong with BSE input file?
Thanks
Yadong Wei
Department of Physics
Harbin Institute of Technology,150001
Yadong Wei
weiyd@hit.edu.cn
Department of Physics
Harbin Institute of Technology,150001
Yadong Wei
 
Posts: 7
Joined: Fri Jun 08, 2018 3:50 am
Location: Harbin,China PR

Re: BSE result not compatible with ypp input

Postby Daniele Varsano » Sat Nov 03, 2018 8:55 pm

Dear Yadong Wei,

I opened the WRbsWF and included the spin-orbit coupling using pwscf before solving BSE, and there exists ndb.BS_diago_Q01 in my 2D_WR_WC directory after completing the BSE calculation.

Actually, I do not understand what you mean with the procedure above.

What version of the code are you running?

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/
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Posts: 2027
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Re: BSE result not compatible with ypp input

Postby Daniele Varsano » Sat Nov 03, 2018 8:55 pm

Dear Yadong Wei,

I opened the WRbsWF and included the spin-orbit coupling using pwscf before solving BSE, and there exists ndb.BS_diago_Q01 in my 2D_WR_WC directory after completing the BSE calculation.

Actually, I do not understand what you mean with the procedure above.

What version of the code are you running?

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/
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Posts: 2027
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Re: BSE result not compatible with ypp input

Postby Yadong Wei » Sun Nov 04, 2018 1:35 am

Dear Daniele:
I am running with yambo-4.3.0 and got error message when doing ypp to analyse the excitons in 2D system.
[ERROR] STOP signal received while in :[06] Excitonic Properties
[ERROR] ndb.BSS_diago, SEC 1, not compatible with ypp input
But the file ndb.BSS_diago was created normally when doing BSE calculation.
I don't know what the problem is, is there the wrong script in my yambo_BSE.in file?
Thank you
Yadong Wei
Yadong Wei
weiyd@hit.edu.cn
Department of Physics
Harbin Institute of Technology,150001
Yadong Wei
 
Posts: 7
Joined: Fri Jun 08, 2018 3:50 am
Location: Harbin,China PR

Re: BSE result not compatible with ypp input

Postby Daniele Varsano » Sun Nov 04, 2018 9:35 am

Dear Yadong Wei,
please sign your post with your affiliation, you can d that once for all by filling the signature field in the user profile.
Actually I can't see anything wrong in your input file. Here something to check:
1) Do you have a ypp.in file in your directory? If so, please rename it and rerun ypp (ypp -e s -J 2D_WR_WC).
2) Please check your yambo run terminated correctly, beside the ndb.* do you have meaningful ouptut file (absortpion etc.?).
3) If none of these are the case, we would need to reproduce the error, so I will ask you to send us your input file possibly for a quick run case.

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/
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Daniele Varsano
 
Posts: 2027
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Re: BSE result not compatible with ypp input

Postby Yadong Wei » Sun Nov 04, 2018 11:27 am

Dear Daniele:
1) I rerun ypp without ypp.in this time (ypp -e s -J 2D_WR_WC) and the same error message shows again with "imcompatible ypp input".
2) BSE calculation done normally with output file
o-2D_WR_WC.eel_q1_diago_bse
o-2D_WR_WC.eps_q1_diago_bse
o-2D_WR_WC.jdos_q1_diago_bse
and r-2D_WR_WC_optics_bse_bsk_bss_em1d_ppa_rim_cut
3) Maybe Quantum Espresso input file is needed reproducing the error ? My input file including scf(10.in) and nscf(wfn.in) also attached, quantum espresso version is 5.4.

Thanks
Yadong
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Yadong Wei
weiyd@hit.edu.cn
Department of Physics
Harbin Institute of Technology,150001
Yadong Wei
 
Posts: 7
Joined: Fri Jun 08, 2018 3:50 am
Location: Harbin,China PR

Re: BSE result not compatible with ypp input

Postby Yadong Wei » Tue Nov 06, 2018 5:29 pm

Dear Developers
From then I searched the report of ypp error. The result "SEC I not compatible by ypp" was generated by the code ./ypp/excitons/excitons_driver.F line 134:
Code: Select all
  call io_control(ACTION=OP_RD_CL,COM=REP,MODE=VERIFY,SEC=(/i_sec/),ID=io_ID)
  io_err=io_BSS_diago(iq,io_ID,Xbsk,BS_E,BS_R_left,BS_R_right,BS_E_SOC_corr,BS_R_kerr,BS_R_PL)
   if (io_err/=0) call error(' ndb.BSS_diago, SEC '//trim(intc(i_sec))//', not compatible with ypp input')

So adding "#" to make the "if" line be a comment and recompiling ypp could temporarily solve the problem and continue analyzing the result. But I thought there must be errors with that. So what does the line "io_err" mean in the code ? Maybe a criterion to prove the BSE result right?
Thanks
Yadong Wei
weiyd@hit.edu.cn
Department of Physics
Harbin Institute of Technology,150001
Yadong Wei
 
Posts: 7
Joined: Fri Jun 08, 2018 3:50 am
Location: Harbin,China PR

Re: BSE result not compatible with ypp input

Postby Daniele Varsano » Tue Nov 06, 2018 7:16 pm

Dear Yadong,
sure that's the line of the code. There the code does some checks and should not stop in your case. We will inspect what the problem is, up to now we did not have time. Commenting that line you can go on even if it could be dangerous in other runlevels.

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/
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Re: BSE result not compatible with ypp input

Postby Davide Sangalli » Fri Nov 09, 2018 1:57 pm

Dear Yadong Wei,
your fix should be working fine in your case.

The error you are getting is just because when loading the ndb.BSS_diago ypp does not know the number of RIM_ng and RIM_n_rand_pts.
So the variables are set to zero.
It does a check and finds out that the value is not consistent with what written in the ndb.BSS_diago and refuses to use the ndb which is instead perfectly fine.
A more proper fix is the following:

Code: Select all
diff --git a/src/io/variables_BS.F b/src/io/variables_BS.F
index c75742fb2..0dc606db3 100644
--- a/src/io/variables_BS.F
+++ b/src/io/variables_BS.F
@@ -211,11 +211,11 @@ integer function variables_BS(ID,local_description,X)
    call io_elemental(ID,VAR="W_DbGd",VAR_SZ=2,MENU=0)
    i_local_desc=i_local_desc+1
    call io_elemental(ID,I0=RIM_ng,&
-&     VAR=' RIM|RL components      [col]:',CHECK=.true.,OP=(/"=="/),&
+&     VAR=' RIM|RL components      [col]:',WARN=.true.,OP=(/"=="/),&
 &     DESCRIPTION=local_description(i_local_desc),DO_NOT_DUMP=.TRUE.)
    i_local_desc=i_local_desc+1
    call io_elemental(ID,I0=RIM_n_rand_pts,&
-&     VAR='    |Random points      [col]:',CHECK=.true.,OP=(/"=="/),&
+&     VAR='    |Random points      [col]:',WARN=.true.,OP=(/"=="/),&
 &     DESCRIPTION=local_description(i_local_desc),DO_NOT_DUMP=.TRUE.)
    !
  endif


Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.ism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/
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Davide Sangalli
 
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