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ypp, band interpolation, time-reversal symmetry

https://www.yambo-code.eu/forum/viewtopic.php?t=1051

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ypp, band interpolation, time-reversal symmetry

Posted: Mon Jul 13, 2015 4:44 pm
by lora_silva
Hello

I am trying to use ypp (new version of Yambo v4.0.0 and v4.0.1) to interpolate the band-structure of some materials and I run into always the same error :
'At line 618 of file mod_com.f90
Fortran runtime error: End of record.'

Therefore, I am redoing the Si band-structure calculation with the new version of yambo to compare with version 3.4.1 (which I had previously obtained a Si band-structure without problems). Since Yambo was upgraded to the new version, one needs to disable the time reversal symmetry in the k-point generation in PWscf QE beforehand, or else when trying to interpolate the band-structure interpolation, ypp complains that time-inversion symmetry needs to be broken and should be define in the input

Code: Select all

fixsyms                      # [R] Reduce Symmetries
RmAllSymm                    # Remove all symmetries
RmTimeRev                    # Remove Time Reversal
This results sometimes of 'segmentation fault' messages, which I presume is because of running out of memory allocation.

In order to avoid this, and for the Si system, I therefore define in the input QE the following (among other variables):

Code: Select all

nosym = .false.,
noinv=.true.
I then convert the wave functions to Yambo format with p2y (since the -S option is not in use anymore for the new yambo v4). After initialisating the G-vectors, I perform a PPA calculation by defining yambo -d -k hartree -g n -p p (without any problems at all, and quite fast with the super-parallel version of Yambo), by using the following input file:

Code: Select all

em1d                         # [R Xd] Dynamical Inverse Dielectric Matrix
gw0                          # [R GW] GoWo Quasiparticle energy levels
ppa                          # [R Xp] Plasmon Pole Approximation
HF_and_locXC                 # [R XX] Hartree-Fock Self-energy and Vxc
X_all_q_ROLEs= "q k c v"            # [PARALLEL] CPUs roles (q,k,c,v)
X_all_q_CPU= "8 8 9 1"              # Parallelism over q points only
SE_ROLEs= "q qp b"
SE_CPU= "8 8 9"                     # Parallilism over q points only
EXXRLvcs=  15        Ry    # [XX] Exchange RL components
Chimod= "hartree"            # [X] IP/Hartree/ALDA/LRC/BSfxc
% BndsRnXp
   1 | 200 |                 # [Xp] Polarization function bands
%
NGsBlkXp= 7            RL    # [Xp] Response block size
% LongDrXp
 1.000000 | 0.000000 | 0.000000 |        # [Xp] [cc] Electric Field
%
PPAPntXp= 27.21138     eV    # [Xp] PPA imaginary energy
% GbndRnge
   1 | 50 |                 # [GW] G[W] bands range
%
GDamping= 0.100000     eV    # [GW] G[W] damping
dScStep= 0.100000      eV    # [GW] Energy step to evalute Z factors
GTermKind= "BRS"            # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
DysSolver= "n"               # [GW] Dyson Equation solver (`n`,`s`,`g`)
%QPkrange                    # [GW] QP generalized Kpoint/Band indices
  1| 73|  1|40|
%
I must add that some parameters haven't been converged against the band-gaps, such as the response block. Since, I want to perform a band-structure interpolation I am taking into account all the QP, which is 73 in total, and I am accounting that the QP corrections be applied on 40 bands.

When using ypp, to interpolate the band structure (ypp -s b -V qp to include GfnQPdb= "E < SAVE/ndb.QP"), with the following input file:

Code: Select all

bnds                         # [R] Bands
electrons                    # [R] Electrons (and holes)
cooIn= "rlu"                 # Points coordinates (in) cc/rlu/iku/alat
BANDS_steps=30                # Number of divisions
% INTERPGrid
-1 |-1 |-1 |                             # Interpolation BZ Grid
%
ShellFac= 20.00000           # The bigger it is a higher number of shells is used
GfnQPdb= "E < SAVE/ndb.QP"              # [EXTQP G] Database
GfnQPdb= "none"              # [EXTQP G] Database
GfnQP_N= 1                   # [EXTQP G] Interpolation neighbours
% GfnQP_E
 0.000000 | 1.000000 | 1.000000 |        # [EXTQP G] E parameters  (c/v) eV|adim|adim
%
GfnQP_Z= ( 1.000000 , 0.000000 )       # [EXTQP G] Z factor  (c/v)
GfnQP_Wv_E= 0.000000   eV    # [EXTQP G] W Energy reference  (valence)#% GfnQP_Wv
 0.00     | 0.00     | 0.00     |        # [EXTQP G] W parameters  (valence) eV|adim|eV^-1
%GfnQP_Wc_E= 0.000000   eV    # [EXTQP G] W Energy reference  (conduction)
% GfnQP_Wc
 0.00     | 0.00     | 0.00     |        # [EXTQP G] W parameters  (conduction) eV|adim|eV^-1
%
%QPkrange                    #  generalized Kpoint/Band indices
  1| 73|  1|40|
%
%BKpts                       # K points of the bands circuit
 0.50     | 0.25     | 0.75     |        # Bands circuit W
 0.00     | 0.00     | 0.00     |        # Bands circuit G
 0.50     | 0.00     | 0.50     |        # Bands circuit X
 0.50     | 0.25     | 0.75     |        # Bands circuit W
 0.50     | 0.50     | 0.50     |        # Bands circuit L
 0.00     | 0.00     | 0.00     |        # Bands circuit G
%
I obtain the output error related to the mod_com.f90 routine, and the l_error file contains the following message:

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 __   __  _______  __   __  _______  _______
|  | |  ||   _   ||  |_|  ||  _    ||       |
|  |_|  ||  |_|  ||       || |_|   ||   _   |
|       ||       ||       ||       ||  | |  |
|_     _||       ||       ||  _   | |  |_|  |
  |   |  |   _   || ||_|| || |_|   ||       |
  |___|  |__| |__||_|   |_||_______||_______|


 <---> P0001: [01] CPU structure, Files & I/O Directories
 <---> P0001: CPU-Threads:96(CPU)-1(threads)
 <---> P0001: [02] Y(ambo) P(ost)/(re) P(rocessor)
 <---> P0001: [03] Core DB
 <---> P0001: :: Electrons             : 8.000000
 <---> P0001: :: Temperature       [ev]: 0.000000
 <---> P0001: :: Lattice factors [a.u.]: 5.152797  5.152797  5.152797
 <---> P0001: :: K points              :  73
 <---> P0001: :: Bands                 : 200
 <---> P0001: :: Symmetries            : 24
 <---> P0001: :: RL vectors            :  9721
 <---> P0001: [04] K-point grid
 <01s> P0001: :: Q-points   (IBZ):  73
 <01s> P0001: :: X K-points (IBZ):  73
 <01s> P0001: [05] CORE Variables Setup
 <01s> P0001: [05.01] Unit cells
 <01s> P0001: [05.02] Symmetries
 <01s> P0001: [WARNING]Spatial Inversion not found among the given symmetry list
 <01s> P0001: [05.03] RL shells
 <01s> P0001: [05.04] K-grid lattice
 <02s> P0001: [05.05] Energies [ev] & Occupations
 <02s> P0001: [06] Interpolation tool
 <02s> P0001: [WARNING]Bands range reduced
 <02s> P0001: Number of K-points in the circuit :  6
 <02s> P0001: [07] External QP corrections (G)
 <02s> P0001: [QP@G] E<SAVE/ndb.QP[ PPA XG:9 Xb:1  200 Scb:1   50]
 <02s> P0001: [INTERPOLATION] Number of shells:   970
Two band files are outputed (o.bands_built_in and o.bands_interpolated), which when plotting the respective data, these produce very strange band-structures. I have reduced the ShellFac to lower values, but it doesn't seem to fix the problem. If I interpolate to fewer bands only one o.band file is outputed, but also producing a similar and strange band structure.

After the GW calculation, there is a warning in the r_em1d_ppa_HF_and_locXC_gw0 file, which is related to the spatial symmetry problem: ' [WARNING]Spatial Inversion not found among the given symmetry list'. This is the only warning produced in this output file.

May the ypp band interpolation problem be related to the symmetry of the system (although I have tried this as well for a perfect cubic system, not resulting in the Spatial inversion symmetry warning, but producing very bad band structures as well)? Can this be related to allocation problems? May someone kindly recommend some other options to solve this problem?

I appreciate any help regarding this issue
Lora Silva
PhD student
Department of Chemistry
University of Bath

Re: ypp, band interpolation, time-reversal symmetry

Posted: Mon Jul 13, 2015 5:17 pm
by Daniele Varsano
Dear Lora,
ypp interpolation tools need surely some improvements.
We will have a look to your problem, in the meanwhile please note that:

Code: Select all

X_all_q_CPU= "8 8 9 1"
and

Code: Select all

SE_CPU= "8 8 9"

are quite dangerous, the parallelism is meant for all entries there ars power of 2.

Best,
Daniele

Re: ypp, band interpolation, time-reversal symmetry

Posted: Tue Jul 14, 2015 8:45 am
by elora
Dear Daniele
Thank-you for your comment. I used this parallel scheme since I was using a supercomputer that has 24 procs in one node: hence, I thought best to use a scheme resulting in a multiple of 24 to take advantage of all the procs. Anyways, I will take your comment under consideration for further calculations.

Regards
Lora

Re: ypp, band interpolation, time-reversal symmetry

Posted: Tue Jul 14, 2015 3:34 pm
by Menico88
Hello

I am also trying to use ypp (new version of Yambo v4.0.0 and v4.0.1 rev88) to interpolate Germanium bulk band-structure just to learn
how to use Yambo properly, and I found the same error message.

Code: Select all

At line 618 of file mod_com.f90
Fortran runtime error: End of record
I removed the Time-reversal symmetry and then I did a COHSEX calculation which ended without any error or warning.

When I launched "ypp -F bands.in"

Code: Select all

#                                                           
#                                                           
# Y88b    /   e           e    e      888~~\    ,88~-_      
#  Y88b  /   d8b         d8b  d8b     888   |  d888   \     
#   Y88b/   /Y88b       d888bdY88b    888 _/  88888    |    
#    Y8Y   /  Y88b     / Y88Y Y888b   888  \  88888    |    
#     Y   /____Y88b   /   YY   Y888b  888   |  Y888   /     
#    /   /      Y88b /          Y888b 888__/    `88_-~      
#                                                           
#                                                           
#             GPL Version 4.0.1 Revision 88                 
#                    MPI+OpenMP Build                       
#               http://www.yambo-code.org                   
#
bnds                         # [R] Bands
electrons                    # [R] Electrons (and holes)
cooIn= "rlu"                 # Points coordinates (in) cc/rlu/iku/alat
% BKpts
 0.50     | 0.50     | 0.50     |     # Bands circuit    
 0.00     | 0.00     | 0.00     |        
 0.50     | 0.50     | 0.00     |        
 0.50     | 0.75     | 0.25     |        
 0.00     | 0.00     | 0.00     |       
%
BANDS_steps=200                # Number of divisions
% INTERPGrid
-1 |-1 |-1 |                             # Interpolation Grid
%
ShellFac= 20.00000           # The bigger it is a higher number of shells is used
GfnQPdb= "E < ./SAVE/ndb.QP"              # [EXTQP G] Database
GfnQP_N= 1                    # [EXTQP G] Interpolation neighbours
% GfnQP_E
 0.000000 | 1.000000 | 1.000000 |        # [EXTQP G] E parameters  (c/v) eV|adim|adim
%
GfnQP_Z= ( 1.000000 , 0.000000 )       # [EXTQP G] Z factor  (c/v)
GfnQP_Wv_E= 0.000000   eV    # [EXTQP G] W Energy reference  (valence)
% GfnQP_Wv
 0.00     | 0.00     | 0.00     |        # [EXTQP G] W parameters  (valence) eV|adim|eV^-1
%
GfnQP_Wc_E= 0.000000   eV    # [EXTQP G] W Energy reference  (conduction)
% GfnQP_Wc
 0.00     | 0.00     | 0.00     |        # [EXTQP G] W parameters  (conduction) eV|adim|eV^-1
%
%QPkrange                    #  generalized Kpoint/Band indices
  1| 22|  1| 20|
%
%BKpts                       # K points of the bands circuit
0.00000 |0.00000 |0.00000 |
%
The output is

Code: Select all

 <---> [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             : 8.000000
 <---> :: Temperature       [ev]: 0.000000
 <---> :: Lattice factors [a.u.]: 5.334696  5.334696  5.334696
 <---> :: K points              : 22
 <---> :: Bands                 :  80
 <---> :: Symmetries            : 24
 <---> :: RL vectors            : 10417
 <---> [04] K-point grid
 <---> :: Q-points   (IBZ): 22
 <---> :: X K-points (IBZ): 22
 <---> [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] Interpolation tool
 <01s> Number of K-points in the circuit :  5
 <01s> [07] External QP corrections (G)
 <01s> [QP@G] E<./SAVE/ndb.QP[ XG:181 Xb:1   80]
 <01s> [INTERPOLATION] Number of shells:  230 [INTERPOLATION] Errors: Max, Avg, Avg_rel =   1.22189522E-06  1.31750397E-07  1.79794120E-06
At line 618 of file mod_com.f90
Fortran runtime error: End of record
The same message such as

Here are the "setup" output and the COHSEX input
"setup"

Code: Select all

                                                                
    ooooo   oooo ..     ooo        ooo ooooooooo.    .oooo.     
     `88.   .8" .88.    `88.       .88 `88"   `Y8b  dP"  `Yb    
      `88. .8" .8"88.    888b     d"88  88     888 88      88   
       `88.8" .8" `88.   8 Y88. .P  88  88oooo888" 88      88   
        `88" .88ooo888.  8  `888"   88  88    `88b 88      88   
         88 .8"     `88. 8    Y     88  88    .88P `8b    d8"   
        o88o88o      888o8          88 o88bood8P"   `Ybod8P"    
                                                                
                                                                
                  GPL Version 4.0.1 Revision 88                 
                        MPI+OpenMP Build                        
                    http://www.yambo-code.org                   
 
 07/14/2015 at 09:51 YAMBO @ hpc1

 [01] CPU structure, Files & I/O Directories
 ===========================================

 * CPU             : 1
 * THREADS    (max): 1
 * THREADS TOT(max): 1
 * I/O NODES       : 1
 * Fragmented I/O  :yes

 CORE databases in   .
 Additional I/O in   .
 Communications in   .
 Input file     is   (none)
 Report file    is   ./r_setup_01
  
 [RD./SAVE//ns.db1]------------------------------------------
  Bands                           :  80
  K-points                        : 22
  G-vectors             [RL space]: 10417
  Components       [wavefunctions]: 1313
  Symmetries             [spatial]: 24
  Spinor components               : 2
  Spin polarizations              : 1
  Temperature                 [ev]: 0.000000
  Electrons                       : 8.000000
  WF G-vectors                    : 1788
  Max atoms/species               : 2
  No. of atom species             : 1
  Magnetic symmetries             : no
 - S/N 007851 --------------------------- v.04.00.00 r.0078 -

 [02] CORE Variables Setup
 =========================


  [02.01] Unit cells
  ==================

  Unit cell is Unknown

  ... containing 2Ge atoms

  ... with scaling factors [a.u.]: 5.334696  5.334696  5.334696

  Direct Lattice(DL) unit cell [iru  /  cc(a.u.)]
  A1 =-1.000000  0.000000  1.000000     -5.334696  0.000000  5.334696
  A2 = 0.000000  1.000000  1.000000      0.000000  5.334696  5.334696
  A3 =-1.000000  1.000000  0.000000     -5.334696  5.334696  0.000000

  DL volume [au]: 303.6401

  Reciprocal Lattice(RL) unit cell [iku  /  cc]
  B1 =-0.500000 -0.500000  0.500000     -0.588898 -0.588898  0.588898
  B2 = 0.500000  0.500000  0.500000      0.588898  0.588898  0.588898
  B3 =-0.500000  0.500000 -0.500000     -0.588898  0.588898 -0.588898


  [02.02] Symmetries
  ==================

  DL (S)ymmetries [cc]
  [S1] 1.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  1.000000
  [S2]-1.000000  0.000000  0.000000  0.000000 -1.000000  0.000000  0.000000  0.000000  1.000000
  [S3]-1.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 -1.000000
  [S4] 1.000000  0.000000  0.000000  0.000000 -1.000000  0.000000  0.000000  0.000000 -1.000000
  [S5] 0.000000  0.000000  1.000000  1.000000  0.000000  0.000000  0.000000  1.000000  0.000000
  [S6] 0.000000  0.000000 -1.000000 -1.000000  0.000000  0.000000  0.000000  1.000000  0.000000
  [S7] 0.000000  0.000000 -1.000000  1.000000  0.000000  0.000000  0.000000 -1.000000  0.000000
  [S8] 0.000000  0.000000  1.000000 -1.000000  0.000000  0.000000  0.000000 -1.000000  0.000000
  [S9] 0.000000  1.000000  0.000000  0.000000  0.000000  1.000000  1.000000  0.000000  0.000000
  [S10] 0.000000 -1.000000  0.000000  0.000000  0.000000 -1.000000  1.000000  0.000000  0.000000
  [S11] 0.000000 -1.000000  0.000000  0.000000  0.000000  1.000000 -1.000000  0.000000  0.000000
  [S12] 0.000000  1.000000  0.000000  0.000000  0.000000 -1.000000 -1.000000  0.000000  0.000000
  [S13] 0.000000 -1.000000  0.000000 -1.000000  0.000000  0.000000  0.000000  0.000000  1.000000
  [S14] 0.000000  1.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  1.000000
  [S15] 0.000000  1.000000  0.000000 -1.000000  0.000000  0.000000  0.000000  0.000000 -1.000000
  [S16] 0.000000 -1.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000 -1.000000
  [S17] 0.000000  0.000000 -1.000000  0.000000  1.000000  0.000000 -1.000000  0.000000  0.000000
  [S18] 0.000000  0.000000  1.000000  0.000000  1.000000  0.000000  1.000000  0.000000  0.000000
  [S19] 0.000000  0.000000  1.000000  0.000000 -1.000000  0.000000 -1.000000  0.000000  0.000000
  [S20] 0.000000  0.000000 -1.000000  0.000000 -1.000000  0.000000  1.000000  0.000000  0.000000
  [S21] 1.000000  0.000000  0.000000  0.000000  0.000000 -1.000000  0.000000 -1.000000  0.000000
  [S22] 1.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  1.000000  0.000000
  [S23]-1.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000 -1.000000  0.000000
  [S24]-1.000000  0.000000  0.000000  0.000000  0.000000 -1.000000  0.000000  1.000000  0.000000

  [SYMs] K-space Time-reversal not included

  [WARNING]Spatial Inversion not found among the given symmetry list
  [SYMs] Group table built correctly

  [02.03] RL shells
  =================

  Shells, format: [S#] G_RL(mHa)

   [S156]:10417(0.7976E+5) [S155]:10369(0.7959E+5) [S154]:10177(0.7907E+5) [S153]:10081(0.7838E+5)
   [S152]:9985(0.7820E+5) [S151]:9841(0.7682E+5) [S150]:9721(0.7630E+5) [S149]:9577(0.7560E+5)
   [S148]:9505(0.7543E+5) [S147]:9409(0.7491E+5) [S146]:9377(0.7422E+5) [S145]:9305(0.7404E+5)
   [S144]:9257(0.7352E+5) [S143]:9185(0.7283E+5) [S142]:9089(0.7265E+5) [S141]:8873(0.7213E+5)
   [S140]:8801(0.7127E+5) [S139]:8657(0.7075E+5) [S138]:8609(0.7005E+5) [S137]:8441(0.6988E+5)
   [S136]:8393(0.6936E+5) [S135]:8363(0.6867E+5) [S134]:8291(0.6849E+5) [S133]:8099(0.6797E+5)
   [S132]:7991(0.6728E+5) [S131]:7943(0.6711E+5) [S130]:7823(0.6659E+5) [S129]:7799(0.6572E+5)
   ...
   [S12]:181( 5549.) [S11]:169( 4682.) [S10]:137( 4162.) [S9]:113( 3468.)
   [S8]:89( 3295.) [S7]:65( 2774.) [S6]:59( 2081.) [S5]:51( 1907.)
   [S4]:27( 1387.) [S3]:15( 693.6022) [S2]:9( 520.2017) [S1]:1( 0.000000)

  [02.04] K-grid lattice
  ======================

  Compatible Grid is 3D
  B1 [rlu]= 0.000000 -0.166667  0.000000
  B2      = 0.000000  0.000000  0.166667
  B3      = 0.166667  0.000000  0.000000
  Grid dimensions               :  6   6   6
  K lattice UC volume       [au]:   0.0038

  [02.05] Energies [ev] & Occupations
  ===================================

  Fermi Level        [ev]:  0.000000
  VBM / CBm          [ev]:   0.00000   0.09609
  Electronic Temp. [ev K]:  0.00      0.00    
  Bosonic    Temp. [ev K]:  0.00      0.00    
  El. density      [cm-3]: 0.178E+24
  States summary         : Full        Metallic    Empty
                           0001-0008               0009-0080
  Indirect Gaps      [ev]:  0.09609   3.92171
  Direct Gaps        [ev]: 0.114126  6.366624
  X BZ K-points : 216

  Energy unit is electronVolt [eV]

  *X* K [1] : 0.000000  0.000000  0.000000 (rlu) * Comp.s 1291 * weight    0.0046
              0.000000  0.000000  0.000000 (iku)
  E -12.88139 -12.88139  -0.31220  -0.31220   0.00000   0.00000   0.00000   0.00000
  E  0.114126  0.114126  2.295565  2.295565  2.525106  2.525106  2.525106  2.525106
  E   6.42913   6.42913   9.36805   9.36805   9.36805   9.36805  10.85057  10.85057
  E  10.89182  10.89182  10.89182  10.89182  13.67250  13.67250  25.26322  25.26322
  E  25.27308  25.27308  25.27308  25.27308  26.43796  26.43796  26.47755  26.47755
   
  *X* K [2] : 0.000000  0.000000  0.166667 (rlu) * Comp.s 1303 * weight   0.01852
              -0.08333   0.08333  -0.08333 (iku)
  E -12.54792 -12.54792  -3.28271  -3.28271  -0.72780  -0.72780  -0.52729  -0.52729
  E  0.937068  0.937068  3.079086  3.079086  3.237973  3.237973  4.190269  4.190269
  E   7.86346   7.86346   8.24431   8.24431   8.24767   8.24767  10.01412  10.01412
  E  13.34449  13.34449  13.36903  13.36903  16.04062  16.04062  21.09153  21.09153
  E  21.16562  21.16562  21.35242  21.35242  26.15774  26.15774  26.16539  26.16539
   
  *X* K [3] : 0.000000  0.000000  0.333333 (rlu) * Comp.s 1308 * weight   0.01852
             -0.166667  0.166667 -0.166667 (iku)
  E -11.62569 -11.62569  -6.22357  -6.22357  -1.36216  -1.36216  -1.16529  -1.16529
  E  0.338267  0.338267  3.595468  3.595468  3.728296  3.728296  7.080348  7.080348
  E   7.92066   7.92066   8.93458   8.93458   8.97244   8.97244  12.71853  12.71853
  E  15.95996  15.95996  16.01484  16.01484  17.27410  17.27410  17.60978  17.60978
  E  17.63638  17.63638  20.37017  20.37017  26.43476  26.43476  26.51781  26.51781
   
  *X* K [4] : 0.000000  0.000000 -0.500000 (rlu) * Comp.s 1308 * weight   0.01852
              0.250000 -0.250000  0.250000 (iku)
  E -10.81789 -10.81789  -7.72627  -7.72627  -1.59406  -1.59406  -1.39759  -1.39759
  E   0.09609   0.09609   3.54645   3.54645   3.65806   3.65806   7.03851   7.03851
  E  10.69928  10.69928  11.45696  11.45696  11.56019  11.56019  11.57583  11.57583
  E  12.39002  12.39002  12.39251  12.39251  19.47813  19.47813  20.88430  20.88430
  E  22.10150  22.10150  22.10175  22.10175  22.55574  22.55574  22.59988  22.59988
   
  *X* K [5] : 0.000000  0.166667  0.166667 (rlu) * Comp.s 1307 * weight   0.02778
              0.000000  0.166667  0.000000 (iku)
  E -12.43318 -12.43318  -3.28009  -3.28009  -1.44602  -1.44602  -1.36197  -1.36197
  E  1.430988  1.430988  2.816768  2.816768  4.355270  4.355270  4.378638  4.378638
  E   6.77395   6.77395   8.47769   8.47769   9.88141   9.88141  11.82352  11.82352
  E  11.83942  11.83942  12.58168  12.58168  17.56632  17.56632  20.54196  20.54196
  E  20.63326  20.63326  22.04039  22.04039  22.55043  22.55043  25.74958  25.74958
   
  *X* K [6] : 0.000000  0.166667  0.333333 (rlu) * Comp.s 1305 * weight   0.05556
              -0.08333  0.250000  -0.08333 (iku)
  E -11.68410 -11.68410  -5.54939  -5.54939  -2.41933  -2.41933  -2.00132  -2.00132
  E  1.642101  1.642101  3.131531  3.131531  4.807956  4.807956  5.241163  5.241163
  E   8.63807   8.63807   9.77050   9.77050  10.30474  10.30474  12.19738  12.19738
  E  14.63305  14.63305  16.14879  16.14879  16.22552  16.22552  16.68114  16.68114
  E  20.83942  20.83942  21.75859  21.75859  22.09645  22.09645  23.68702  23.68702
   
  *X* K [7] : 0.000000  0.166667 -0.500000 (rlu) * Comp.s 1292 * weight   0.05556
              0.333333 -0.166667  0.333333 (iku)
  E -10.64059 -10.64059  -7.53235  -7.53235  -3.25165  -3.25165  -2.06471  -2.06471
  E  1.515257  1.515257  3.723366  3.723366  4.887911  4.887911  6.380959  6.380959
  E   9.22526   9.22526  11.28176  11.28176  11.43408  11.43408  12.20369  12.20369
  E  13.05202  13.05202  16.76118  16.76118  18.42542  18.42542  19.22950  19.22950
  E  20.52556  20.52556  21.39007  21.39007  22.80330  22.80330  23.69203  23.69203
   
  *X* K [8] : 0.000000  0.166667 -0.333333 (rlu) * Comp.s 1299 * weight   0.05556
              0.250000  -0.08333  0.250000 (iku)
  E -10.96922 -10.96922  -6.99768  -6.99768  -3.45848  -3.45848  -1.57710  -1.57710
  E  1.691631  1.691631  3.949934  3.949934  4.364409  4.364409  6.790087  6.790087
  E   8.28603   8.28603   9.16129   9.16129  11.21547  11.21547  13.17226  13.17226
  E  14.80403  14.80403  16.58826  16.58826  16.84148  16.84148  18.41293  18.41293
  E  21.11279  21.11279  22.72168  22.72168  22.97779  22.97779  23.82812  23.82812
   
  *X* K [9] : 0.000000  0.166667 -0.166667 (rlu) * Comp.s 1313 * weight   0.05556
              0.166667 0.139E-16  0.166667 (iku)
  E -12.00690 -12.00690  -4.83923  -4.83923  -2.68394  -2.68394  -0.79070  -0.79070
  E  1.935122  1.935122  3.479905  3.479905  3.701788  3.701788  5.110273  5.110273
  E   7.17953   7.17953   9.46597   9.46597   9.49731   9.49731  11.84981  11.84981
  E  13.22005  13.22005  16.03746  16.03746  16.76970  16.76970  18.82892  18.82892
  E  20.76484  20.76484  21.68003  21.68003  21.74456  21.74456  23.83177  23.83177
   
  *X* K [10] : 0.000000  0.333333  0.333333 (rlu) * Comp.s 1299 * weight   0.02778
               0.000000  0.333333  0.000000 (iku)
  E -11.11553 -11.11553  -6.33373  -6.33373  -2.72235  -2.72235  -2.69163  -2.69163
  E  0.458851  0.458851  1.803722  1.803722  7.356960  7.356960  7.408968  7.408968
  E   8.72960   8.72960  11.41970  11.41970  12.06555  12.06555  14.67929  14.67929
  E  14.68440  14.68440  15.09472  15.09472  15.83527  15.83527  15.93954  15.93954
  E  17.53402  17.53402  18.84701  18.84701  24.33314  24.33314  25.18926  25.18926
   
  *X* K [11] : 0.000000  0.333333 -0.500000 (rlu) * Comp.s 1292 * weight   0.05556
               0.416667  -0.08333  0.416667 (iku)
  E -10.05383 -10.05383  -7.82890  -7.82890  -3.86987  -3.86987  -2.85824  -2.85824
  E  0.847248  0.847248  2.537875  2.537875  7.107657  7.107657  7.675120  7.675120
  E  10.57788  10.57788  11.78322  11.78322  12.37471  12.37471  13.86794  13.86794
  E  14.19107  14.19107  16.42826  16.42826  17.53801  17.53801  18.08857  18.08857
  E  18.84705  18.84705  19.73227  19.73227  20.40154  20.40154  22.97243  22.97243
   
  *X* K [12] : 0.000000  0.333333 -0.333333 (rlu) * Comp.s 1292 * weight   0.05556
               0.333333 -.278E-16  0.333333 (iku)
  E -9.924249 -9.924249 -7.970882 -7.970882 -4.595081 -4.595081 -2.409931 -2.409931
  E  1.271704  1.271704  5.792438  5.792438  6.447175  6.447175  6.509175  6.509175
  E   7.11701   7.11701   8.87371   8.87371  13.92143  13.92143  14.11017  14.11017
  E  16.05975  16.05975  17.62321  17.62321  17.94892  17.94892  19.22115  19.22115
  E  19.31027  19.31027  20.73383  20.73383  22.47741  22.47741  22.50313  22.50313
   
  *X* K [13] : 0.000000 -0.500000 -0.500000 (rlu) * Comp.s 1298 * weight   0.01389
               0.000000 -0.500000  0.000000 (iku)
  E -9.021591 -9.021591 -9.021591 -9.021591 -3.167043 -3.167043 -3.167043 -3.167043
  E  0.530403  0.530403  0.530403  0.530403  9.702533  9.702533  9.702533  9.702533
  E  12.03436  12.03436  12.03436  12.03436  12.86932  12.86932  12.86932  12.86932
  E  13.97618  13.97618  13.97618  13.97618  19.22597  19.22597  19.22597  19.22597
  E  19.43329  19.43329  19.43329  19.43329  19.84066  19.84066  19.84066  19.84066
   
  *X* K [14] : 0.166667  0.333333 -0.500000 (rlu) * Comp.s 1300 * weight  0.111111
               0.333333 -0.166667  0.500000 (iku)
  E -10.77969 -10.77969  -6.89903  -6.89903  -3.83042  -3.83042  -2.56059  -2.56059
  E  2.666012  2.666012  3.200943  3.200943  4.202319  4.202319  7.146630  7.146630
  E   9.37439   9.37439  10.00306  10.00306  12.69780  12.69780  13.36095  13.36095
  E  14.02884  14.02884  16.27407  16.27407  16.57592  16.57592  18.64121  18.64121
  E  19.86483  19.86483  22.21127  22.21127  22.33568  22.33568  22.83328  22.83328
   
  *X* K [15] : 0.166667  0.333333 -0.333333 (rlu) * Comp.s 1290 * weight  0.111111
               0.250000  -0.08333  0.416667 (iku)
  E -9.919671 -9.919671 -8.000018 -8.000018 -4.285811 -4.285811 -3.000822 -3.000822
  E  2.985085  2.985085  3.474523  3.474523  6.036326  6.036326  6.161233  6.161233
  E   8.03623   8.03623  12.03250  12.03250  12.07256  12.07256  12.78538  12.78538
  E  16.79324  16.79324  17.13186  17.13186  17.90153  17.90153  18.92890  18.92890
  E  19.26630  19.26630  21.32041  21.32041  22.15232  22.15232  22.73393  22.73393
   
  *X* K [16] : 0.166667 -0.500000 -0.333333 (rlu) * Comp.s 1290 * weight   0.05556
              -0.166667 -0.500000  0.000000 (iku)
  E -8.959949 -8.959949 -8.939418 -8.939418 -3.896862 -3.896862 -3.825616 -3.825616
  E  2.541008  2.541008  2.601834  2.601834  6.563595  6.563596  6.636079  6.636079
  E  11.12233  11.12233  11.27480  11.27480  13.23123  13.23123  13.32139  13.32139
  E  16.95067  16.95067  16.96437  16.96437  17.56692  17.56692  17.58158  17.58158
  E  18.79342  18.79342  18.81232  18.81232  22.67287  22.67287  22.68314  22.68314
   
  *X* K [17] : 0.000000 -0.333333  0.500000 (rlu) * Comp.s 1292 * weight   0.05556
              -0.416667   0.08333 -0.416667 (iku)
  E -10.05383 -10.05383  -7.82890  -7.82890  -3.86987  -3.86987  -2.85824  -2.85824
  E  0.847248  0.847248  2.537875  2.537875  7.107657  7.107657  7.675120  7.675120
  E  10.57788  10.57788  11.78322  11.78322  12.37471  12.37471  13.86794  13.86794
  E  14.19107  14.19107  16.42826  16.42826  17.53801  17.53801  18.08857  18.08857
  E  18.84705  18.84705  19.73227  19.73227  20.40154  20.40154  22.97243  22.97243
   
  *X* K [18] : 0.000000  0.000000 -0.166667 (rlu) * Comp.s 1303 * weight   0.01852
                0.08333  -0.08333   0.08333 (iku)
  E -12.54792 -12.54792  -3.28271  -3.28271  -0.72780  -0.72780  -0.52729  -0.52729
  E  0.937068  0.937068  3.079086  3.079086  3.237973  3.237973  4.190269  4.190269
  E   7.86346   7.86346   8.24431   8.24431   8.24767   8.24767  10.01412  10.01412
  E  13.34449  13.34449  13.36903  13.36903  16.04062  16.04062  21.09153  21.09153
  E  21.16562  21.16562  21.35242  21.35242  26.15774  26.15774  26.16539  26.16539
   
  *X* K [19] : 0.000000 -0.166667  0.333333 (rlu) * Comp.s 1299 * weight   0.05556
              -0.250000   0.08333 -0.250000 (iku)
  E -10.96922 -10.96922  -6.99768  -6.99768  -3.45848  -3.45848  -1.57710  -1.57710
  E  1.691631  1.691631  3.949934  3.949934  4.364409  4.364409  6.790087  6.790087
  E   8.28603   8.28603   9.16129   9.16129  11.21547  11.21547  13.17226  13.17226
  E  14.80403  14.80403  16.58826  16.58826  16.84148  16.84148  18.41293  18.41293
  E  21.11279  21.11279  22.72168  22.72168  22.97779  22.97779  23.82812  23.82812
   
  *X* K [20] : 0.000000 -0.166667 -0.333333 (rlu) * Comp.s 1305 * weight   0.05556
                0.08333 -0.250000   0.08333 (iku)
  E -11.68410 -11.68410  -5.54939  -5.54939  -2.41933  -2.41933  -2.00132  -2.00132
  E  1.642101  1.642101  3.131531  3.131531  4.807956  4.807956  5.241163  5.241163
  E   8.63807   8.63807   9.77050   9.77050  10.30474  10.30474  12.19738  12.19738
  E  14.63305  14.63305  16.14879  16.14879  16.22552  16.22552  16.68114  16.68114
  E  20.83942  20.83942  21.75859  21.75859  22.09645  22.09645  23.68702  23.68702
   
  *X* K [21] : 0.000000  0.000000 -0.333333 (rlu) * Comp.s 1308 * weight   0.01852
               0.166667 -0.166667  0.166667 (iku)
  E -11.62569 -11.62569  -6.22357  -6.22357  -1.36216  -1.36216  -1.16529  -1.16529
  E  0.338267  0.338267  3.595468  3.595468  3.728296  3.728296  7.080348  7.080348
  E   7.92066   7.92066   8.93458   8.93458   8.97244   8.97244  12.71853  12.71853
  E  15.95996  15.95996  16.01484  16.01484  17.27410  17.27410  17.60978  17.60978
  E  17.63638  17.63638  20.37017  20.37017  26.43476  26.43476  26.51781  26.51781
   
  *X* K [22] : 0.000000 -0.166667  0.500000 (rlu) * Comp.s 1292 * weight   0.05556
              -0.333333  0.166667 -0.333333 (iku)
  E -10.64059 -10.64059  -7.53235  -7.53235  -3.25165  -3.25165  -2.06471  -2.06471
  E  1.515257  1.515257  3.723366  3.723366  4.887911  4.887911  6.380959  6.380959
  E   9.22526   9.22526  11.28176  11.28176  11.43408  11.43408  12.20369  12.20369
  E  13.05202  13.05202  16.76118  16.76118  18.42542  18.42542  19.22950  19.22950
  E  20.52556  20.52556  21.39007  21.39007  22.80330  22.80330  23.69203  23.69203

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


 IBZ Q-points : 22
 BZ  Q-points : 216

 Q [00001] : 0.00      0.00      0.00     (iku) * weight    0.0046
 Q [00002] : -0.08333   0.08333  -0.08333 (iku) * weight   0.01852
 Q [00003] :-0.166667  0.166667 -0.166667 (iku) * weight   0.01852
 Q [00004] : 0.250000 -0.250000  0.250000 (iku) * weight   0.01852
 Q [00005] : 0.000000  0.166667  0.000000 (iku) * weight   0.02778
 Q [00006] : -0.08333   0.25000  -0.08333 (iku) * weight   0.05556
 Q [00007] :-0.166667  0.333333 -0.166667 (iku) * weight   0.05556
 Q [00008] :  0.25000  -0.08333   0.25000 (iku) * weight   0.05556
 Q [00009] : 0.166667  0.000000  0.166667 (iku) * weight   0.05556
 Q [00010] : 0.000000  0.333333  0.000000 (iku) * weight   0.02778
 Q [00011] : -0.08333   0.41667  -0.08333 (iku) * weight   0.05556
 Q [00012] : 0.333333  0.000000  0.333333 (iku) * weight   0.05556
 Q [00013] : 0.000000 -0.500000  0.000000 (iku) * weight   0.01389
 Q [00014] :-0.166667  0.333333  0.000000 (iku) * weight  0.111111
 Q [00015] :  0.25000  -0.08333   0.41667 (iku) * weight  0.111111
 Q [00016] :-.1667    -.5000    0.1265E-7 (iku) * weight   0.05556
 Q [00017] :  0.08333  -0.41667   0.08333 (iku) * weight   0.05556
 Q [00018] :  0.08333  -0.08333   0.08333 (iku) * weight   0.01852
 Q [00019] : -0.25000   0.08333  -0.25000 (iku) * weight   0.05556
 Q [00020] :  0.08333  -0.25000   0.08333 (iku) * weight   0.05556
 Q [00021] : 0.166667 -0.166667  0.166667 (iku) * weight   0.01852
 Q [00022] : 0.166667 -0.333333  0.166667 (iku) * weight   0.05556
  
 Q [00001] : 0.00      0.00      0.00     (cc ) * weight    0.0046
 Q [00002] : -0.09815   0.09815  -0.09815 (cc ) * weight   0.01852
 Q [00003] :-0.196299  0.196299 -0.196299 (cc ) * weight   0.01852
 Q [00004] : 0.294449 -0.294449  0.294449 (cc ) * weight   0.01852
 Q [00005] : 0.000000  0.196299  0.000000 (cc ) * weight   0.02778
 Q [00006] : -0.09815   0.29445  -0.09815 (cc ) * weight   0.05556
 Q [00007] :-0.196299  0.392599 -0.196299 (cc ) * weight   0.05556
 Q [00008] :  0.29445  -0.09815   0.29445 (cc ) * weight   0.05556
 Q [00009] : 0.196299  0.000000  0.196299 (cc ) * weight   0.05556
 Q [00010] : 0.000000  0.392599  0.000000 (cc ) * weight   0.02778
 Q [00011] : -0.09815   0.49075  -0.09815 (cc ) * weight   0.05556
 Q [00012] : 0.392599  0.000000  0.392599 (cc ) * weight   0.05556
 Q [00013] : 0.000000 -0.588898  0.000000 (cc ) * weight   0.01389
 Q [00014] :-0.196299  0.392599  0.000000 (cc ) * weight  0.111111
 Q [00015] :  0.29445  -0.09815   0.49075 (cc ) * weight  0.111111
 Q [00016] :-.1963    -.5889    0.1490E-7 (cc ) * weight   0.05556
 Q [00017] :  0.09815  -0.49075   0.09815 (cc ) * weight   0.05556
 Q [00018] :  0.09815  -0.09815   0.09815 (cc ) * weight   0.01852
 Q [00019] : -0.29445   0.09815  -0.29445 (cc ) * weight   0.05556
 Q [00020] :  0.09815  -0.29445   0.09815 (cc ) * weight   0.05556
 Q [00021] : 0.196299 -0.196299  0.196299 (cc ) * weight   0.01852
 Q [00022] : 0.196299 -0.392599  0.196299 (cc ) * weight   0.05556

 :: Indices: polarization function
 :: Indices: Self-Energy

 [WR./SAVE//ndb.kindx]---------------------------------------
  Polarization last K   : 22
  QP states             :  1  22
  X grid is uniform     :yes
  X grid impose -q      :no
  BS scattering         :no
  COLL scattering       :no
 - S/N 007851 --------------------------- v.04.00.01 r.0088 -

 [04] External corrections
 =========================


 [05] Timing Overview
 ====================

 Routines: global (Only MASTER cpu here)
                io_WF :     0.00s CPU
                io_HF :     0.00s CPU
           io_DIPOLES :     0.00s CPU

 [06] Game Over & Game summary
 =============================

 07/14/2015 at 09:51 YAMBO @ hpc1 [start]
 07/14/2015 at 09:51              [end]

 Timing   [Min/Max/Average]: 01s/01s/01s
              [Time-Profile]:  1.409939s

COHSEX input

Code: Select all

em1s                         # [R Xs] Static Inverse Dielectric Matrix
gw0                          # [R GW] GoWo Quasiparticle energy levels
cohsex                       # [R Xp] COlumb Hole Screened EXchange
HF_and_locXC                 # [R XX] Hartree-Fock Self-energy and Vxc
X_all_q_CPU= ""              # [PARALLEL] CPUs for each role
X_all_q_ROLEs= ""            # [PARALLEL] CPUs roles (q,k,c,v)
X_all_q_nCPU_invert=0        # [PARALLEL] CPUs for matrix inversion
X_Threads= 12                 # [OPENMP/X] Number of threads for response functions
DIP_Threads= 12               # [OPENMP/X] Number of threads for dipoles
SE_CPU= ""                   # [PARALLEL] CPUs for each role
SE_ROLEs= ""                 # [PARALLEL] CPUs roles (q,qp,b)
SE_Threads= 12                # [OPENMP/GW] Number of threads for self-energy
EXXRLvcs= 10       Ry    # [XX] Exchange RL components
Chimod= "hartree"            # [X] IP/Hartree/ALDA/LRC/BSfxc
% BndsRnXs
   1 |  80 |                 # [Xs] Polarization function bands
%
NGsBlkXs= 10            Ry    # [Xs] Response block size
% LongDrXs
 1.000000 | 1.000000 | 1.000000 |        # [Xs] [cc] Electric Field
%
% GbndRnge
   1 |  80 |                 # [GW] G[W] bands range
%
%QPkrange                    # [GW] QP generalized Kpoint/Band indices
  1| 22|  1| 20|
%
%QPerange                    # [GW] QP generalized Kpoint/Energy indices
  1| 22| 0.0|-1.0|
%

I hope I wrote all the information you need.
Thank you very much for your work! :D :D

Kind Regards

Guido Menichetti
PhD Student
Department of Physics
University of Pisa

Re: ypp, band interpolation, time-reversal symmetry

Posted: Thu Jul 23, 2015 8:52 am
by Davide Sangalli
Dear Guido,
can you attach also the input of your DFT run and the pseudopotential ?

Best,
D.

Re: ypp, band interpolation, time-reversal symmetry

Posted: Fri Jul 24, 2015 8:11 am
by Menico88
Dear Davide

Good Morning,

Here are the scf, nscf and Pseudopotential files.

SCF

Code: Select all

&control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='Ge'
    pseudo_dir = './',
    outdir='./SCRATCH/'
    wf_collect=.true.,
    verbosity ='high',
 /
 &system
    ibrav= 2, celldm(1)= 10.669392932, nat= 2, ntyp= 1,
    ecutwfc = 40
    noncolin = .true.
    lspinorb = .true.
    force_symmorphic= .true.,
 /
 &electrons
    diago_thr_init = 1.0e-6
    diago_full_acc = .true.
    !conv_thr =  1.0d-6
    !mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Ge  72.630  Ge.rel-pz-n-nc.UPF
ATOMIC_POSITIONS
 Ge 0.00 0.00 0.00
 Ge 0.25 0.25 0.25
K_POINTS automatic
 6 6 6 0 0 0

NSCF

Code: Select all

&control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='Ge'
    pseudo_dir = './',
    outdir='./SCRATCH/'
    wf_collect=.true.,
    verbosity ='high',
 /
 &system
    ibrav= 2, celldm(1)= 10.669392932, nat= 2, ntyp= 1,
    ecutwfc = 40
    noncolin = .true.
    lspinorb = .true.
    force_symmorphic= .true.,
    nbnd = 80
 /
 &electrons
    diago_thr_init = 1.0e-6
    diago_full_acc = .true.
    !conv_thr =  1.0d-6
    !mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Ge  72.630  Ge.rel-pz-n-nc.UPF
ATOMIC_POSITIONS
 Ge 0.00 0.00 0.00
 Ge 0.25 0.25 0.25
K_POINTS automatic
6 6 6 0 0 0
The Pseudopotential is attached


Thank you for your work

Kind Regards

Guido

Re: ypp, band interpolation, time-reversal symmetry

Posted: Fri Oct 16, 2015 12:38 pm
by Fabiof
Dear Davide

I just would like to know if the problem in the first post has a solution already. I'm getting the segmentation fault when trying to use ypp for interpolating graphene band structure. Even if i use noinv = true, i still get the segmentation problem.

Code: Select all

Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x91000000a0
Segmentation fault

Using the 3.4.1 version i dont have this problem. Should i use 3.4.1 yambo version meanwhile?


Fabio

Re: ypp, band interpolation, time-reversal symmetry

Posted: Fri Oct 23, 2015 4:42 pm
by Daniele Varsano
Dear Fabio,
sorry for the late reply.
Can you post more information (input/output) in order to see at what stage you encounter the error.
Please post also the scf/nscf input of the ground state structure.
Anyway the problem with the symmetry is the time-reversal and you can remove it in post processing stage using ypp.

Daniele

Re: ypp, band interpolation, time-reversal symmetry

Posted: Sat Oct 24, 2015 11:30 am
by Fabiof
Dear Daniele,

Ok, files are attached.

If i add the option to remove symmetry in ypp file, i get the following error

Code: Select all

13s> [WARNING]Global and response function energy levels have different metallic character
 <13s> [INTERPOLATION] Number of shells:   3369Segmentation fault
Fabio

Re: ypp, band interpolation, time-reversal symmetry

Posted: Sat Oct 24, 2015 11:36 am
by Daniele Varsano
Dear Fabio,
Strange enough,
please note the files are not attached. Unfortunately not all the format are allowed to be uploaded, but if you upload a tar.gz or .tgz it should work.
Next note that you do not need to add the symmetry removal in the input file, but first run ypp to remove symmetries and next do the band interpolation.
Anyway, post all the relevant files and let's see is there is something wrong, otherwise I'll ask you the ground state input files in order to reproduce the error.

Best,

Daniele
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