Fail to generate input file

Run-time issues concerning Yambo that are not covered in the above forums.

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ZHuang
Posts: 10
Joined: Sat Jul 08, 2023 3:32 pm

Fail to generate input file

Post by ZHuang » Thu Jul 20, 2023 3:13 am

Dear all,

In my try of GW calculation I cannot generate input file via command $ yambo -x -p p -g n.
I have also reduced to ecutwfc to 25 or set the nspin=1, while the same error occurs.

Below was some information concerning the input and output during my test.

There are some warning information shown during the initialization via $ yambo

Code: Select all

 <---> [WARNING]Merged spin levels are metallic
 <---> [WARNING][X] System is an half-metal
 <---> [WARNING]Merged spin levels are metallic
and

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<---> X [eval] |                                        | [000%] --(E) --(X)
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
and possibly this

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 <---> Null transition detected [qindx_X]. Gamma point only.

My structure is (MA)2CuCl4, where MA is CH3NH3， and the pseduopoential files are downloaded from http://pseudopotentials.quantum-espress ... -hutter-pp

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Cl     35.45270  Cl.pz-hgh.UPF
N      14.00674  N.pz-hgh.UPF
H       1.00794  H.pz-hgh.UPF
C      12.01070  C.pz-hgh.UPF
Cu     63.54600  Cu.pz-d-hgh.UPF
and the SCF file is

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&CONTROL
    calculation = "scf"
    prefix = 'RCU'
    max_seconds =  8.64000e+04
    pseudo_dir  = "../pseudopot_qe"
    wf_collect = .true.
/

&SYSTEM
    a                         =  1.00051e+01
    b                         =  7.35320e+00
    c                         =  7.30950e+00
    cosac                     = -3.62227e-01
    degauss                   =  1.00000e-02
    ecutrho                   =  3.00000e+02
    ecutwfc                   =  7.50000e+01
    ibrav                     = -12
    nat                       = 42
    nspin                     = 2
    ntyp                      = 5
    occupations               = "smearing"
    smearing                  = "gaussian"
    starting_magnetization(1) =  0.00000e+00
    starting_magnetization(2) =  0.00000e+00
    starting_magnetization(3) =  0.00000e+00
    starting_magnetization(4) =  0.00000e+00
    starting_magnetization(5) =  2.00000e-01
    force_symmorphic=.true.
/

&ELECTRONS
    conv_thr         =  1.00000e-06
    diago_david_ndim = 4
    diagonalization  = "david"
    electron_maxstep = 200
    mixing_beta      =  4.00000e-01
    mixing_mode      = "plain"
    mixing_ndim      = 8
    startingpot      = "atomic"
    startingwfc      = "atomic+random"
/

K_POINTS {automatic}
 1  2  2  0 0 0


ATOMIC_SPECIES
Cl     35.45270  Cl.pz-hgh.UPF
N      14.00674  N.pz-hgh.UPF
H       1.00794  H.pz-hgh.UPF
C      12.01070  C.pz-hgh.UPF
Cu     63.54600  Cu.pz-d-hgh.UPF


ATOMIC_POSITIONS {angstrom}
...
After the SCF and NSCF calculation, p2y runs successfuly,

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<---> DBs path set to : .
 <---> detected QE data format : qexsd
 <---> == PWscf v.6.x generated data (QEXSD fmt) ==
 <---> Header/K-points/Energies... done
 <02s> Cell data...
 <02s> [WARNING]Two or more crystal structures fit the given cell done
 <02s> Atomic data... done
 <02s> Symmetries...[SI yes]...[I yes]...[-I yes]...[TR no]
 <03s> XC functional...Slater exchange(X)+Perdew & Zunger(C)
 <03s> EXX fraction...:  0.000000
 <03s> EXX screening...:  0.000000
 <03s> K-points mesh... done
 <03s> RL vectors... done
 <04s> IGK arrays... done
 <04s> Energies... done
 <05s>  Electrons             :  138.0000
 <05s>  Temperature           :  0.950044E-3 [eV]
 <05s>  Lattice factors       :  18.90690  13.89553  12.87491 [a.u.]
 <05s>  K-points              :   56
 <05s>  Bands                 :  200
 <05s>  Spinor components     :  1
 <05s>  Spin polarizations    :  2
 <05s>  Spin orbit coupling    : no
 <05s>  Symmetries   [spatial]:  2
 <05s>                 [T-rev] : no
 <05s>  Max WF components     :   37148
 <05s>  RL vectors        (WF):   41379
 <05s>  RL vectors    (CHARGE):  296757
 <05s>  XC potential           : Slater exchange(X)+Perdew & Zunger(C)
 <05s>  Atomic species        :   5
 <05s>  Max atoms/species     :  24
 <05s> == DB1 (Gvecs and more) ...
 <05s> ... Database done
 <05s> == DB2 (wavefunctions)  ...
 <16s> [p2y] WF I/O |########################################| [100%] 11s(E) 11s(X) done ==
 <27s> == DB3 (PseudoPotential) ... done ==
 <55s>  == P2Y completed ==
Then test the GW calculation following the tutorial at https://www.yambo-code.eu/wiki/index.ph ... rial:_h-BN

Firstly I run the initialization via the command
$ yambo

It seems that the errors have occurred at this 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
 <---> Shells finder |########################################| [100%] --(E) --(X)
 <---> [02.04] K-grid lattice
 <---> Grid dimensions      :   6   6   3
 <---> [02.05] Energies & Occupations
 <---> [WARNING]Merged spin levels are metallic
 <---> [WARNING][X] System is an half-metal
 <---> [WARNING]Merged spin levels are metallic
 <---> [03] Transferred momenta grid and indexing
 <---> BZ -> IBZ reduction |########################################| [100%] --(E) --(X)
 <---> [03.01] X indexes
 <---> X [eval] |                                        | [000%] --(E) --(X)
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> [WARNING] Error search for G=G1-G2 !!
 <---> X [eval] |########################################| [100%] --(E) --(X)
 <---> X[REDUX] |########################################| [100%] --(E) --(X)
 <---> Null transition detected [qindx_X]. Gamma point only.
 <---> [04] Timing Overview
 <---> [05] Game Over & Game summary
Then I tried to get the input file via command
$ yambo -x -p p -g n

Noting was generated by this command, and all output is

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#
#  /$$     /$$ /$$$$$$  /$$      /$$ /$$$$$$$   /$$$$$$
# |  $$   /$$//$$__  $$| $$$    /$$$| $$__  $$ /$$__  $$
#  \  $$ /$$/| $$  \ $$| $$$$  /$$$$| $$  \ $$| $$  \ $$
#   \  $$$$/ | $$$$$$$$| $$ $$/$$ $$| $$$$$$$ | $$  | $$
#    \  $$/  | $$__  $$| $$  $$$| $$| $$__  $$| $$  | $$
#     | $$   | $$  | $$| $$\  $ | $$| $$  \ $$| $$  | $$
#     | $$   | $$  | $$| $$ \/  | $$| $$$$$$$/|  $$$$$$/
#     |__/   |__/  |__/|__/     |__/|_______/  \______/
#
# Version 5.1.0 Revision 21422 Hash (prev commit) fde6e2a07
#                    Branch is (HEAD
#                 MPI+HDF5_MPI_IO Build
#               http://www.yambo-code.org
#
~                                                                                                                  
~                                                                                                                  
~                                                                                                                  
~                                                                                                                  
~

I have also tried the generate the input file of other calculation, for example, $ yambo_nl -u n
what I got is

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#
#  ____  ____     _       ____    ____  ______      ___
# |_  _||_  _|   / \     |_   \  /   _||_   _ \   ."   `.
#   \ \  / /    / _ \      |   \/   |    | |_) | /  .-.  \
#    \ \/ /    / ___ \     | |\  /| |    |  __". | |   | |
#    _|  |_  _/ /   \ \_  _| |_\/_| |_  _| |__) |\  `-"  /
#   |______||____| |____||_____||_____||_______/  `.___."
#
#
#
# Version 5.1.0 Revision 21422 Hash (prev commit) fde6e2a07
#                     Branch is (HEAD
#                  MPI+HDF5_MPI_IO Build
#                http://www.yambo-code.org
#
% Field1_Freq
 0.100000 | 0.100000 |         eV    # [RT Field1] Frequency
%
Field1_Int=  1000.00       kWLm2 # [RT Field1] Intensity
Field1_Width= 0.000000     fs    # [RT Field1] Width
Field1_kind= "SOFTSIN"           # [RT Field1] Kind(SIN|RES|ANTIRES|GAUSS|DELTA|QSSIN)
Field1_pol= "linear"             # [RT Field1] Pol(linear|circular)
% Field1_Dir
 0.000000 | 0.000000 | 0.000000 |        # [RT Field1] Versor
%
% Field1_Dir_circ
 0.000000 | 1.000000 | 0.000000 |        # [RT Field1] Versor_circ
%
Field1_Tstart= 0.010000    fs    # [RT Field1] Initial Time
The input file lack of some information in comparison with that generated from the hBN_2D structure downloaded from the https://www.yambo-code.eu/
The input file generated from the hBN_2D is

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#    #+#  #+#     #+# #+#       #+# #+#    #+# #+#    #+#
#    ###  ###     ### ###       ### #########   ########
#
#
# Version 5.1.0 Revision 21422 Hash (prev commit) fde6e2a07
#                     Branch is (HEAD
#                  MPI+HDF5_MPI_IO Build
#                http://www.yambo-code.org
#
nloptics                         # [R] Non-linear spectroscopy
% NLBands
   1 |  80 |                         # [NL] Bands range
%
NLverbosity= "high"              # [NL] Verbosity level (low | high)
NLtime=-1.000000           fs    # [NL] Simulation Time
NLintegrator= "INVINT"           # [NL] Integrator ("EULEREXP/RK2/RK4/RK2EXP/HEUN/INVINT/CRANKNIC")
NLCorrelation= "IPA"             # [NL] Correlation ("IPA/HARTREE/TDDFT/LRC/LRW/JGM/SEX")
NLLrcAlpha= 0.000000             # [NL] Long Range Correction
% NLEnRange
 0.200000 | 8.000000 |         eV    # [NL] Energy range
%
NLEnSteps= 1                     # [NL] Energy steps
NLDamping= 0.200000        eV    # [NL] Damping (or dephasing)
RADLifeTime=-1.000000      fs    # [RT] Radiative life-time (if negative Yambo sets it equal to Phase_LifeTime in NL)
#EvalCurrent                   # [NL] Evaluate the current
#FrPolPerdic                   # [DIP] Force periodicity of polarization respect to the external field
HARRLvcs= 21817            RL    # [HA] Hartree     RL components
EXXRLvcs= 21817            RL    # [XX] Exchange    RL components
% Field1_Freq
 0.100000 | 0.100000 |         eV    # [RT Field1] Frequency
%
Field1_Int=  1000.00       kWLm2 # [RT Field1] Intensity
Field1_Width= 0.000000     fs    # [RT Field1] Width
Field1_kind= "SOFTSIN"           # [RT Field1] Kind(SIN|RES|ANTIRES|GAUSS|DELTA|QSSIN)
Field1_pol= "linear"             # [RT Field1] Pol(linear|circular)
% Field1_Dir
 0.000000 | 0.000000 | 0.000000 |        # [RT Field1] Versor
%
% Field1_Dir_circ
 0.000000 | 1.000000 | 0.000000 |        # [RT Field1] Versor_circ
%
Field1_Tstart= 0.010000    fs    # [RT Field1] Initial Time
Thank you very much for your help!
Zhipeng Huang
Tongji University
Last edited by ZHuang on Thu Jul 20, 2023 5:20 pm, edited 1 time in total.
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ZHuang
Posts: 10
Joined: Sat Jul 08, 2023 3:32 pm

Re: Fail to generate input file

Post by ZHuang » Thu Jul 20, 2023 8:30 am

The problem has been solved by following the post viewtopic.php?t=1955

Best regards,
Zhipeng Huang
Tongji University
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Daniele Varsano
Posts: 3816
Joined: Tue Mar 17, 2009 2:23 pm
Contact:
Contact Daniele Varsano

Re: Fail to generate input file

Post by Daniele Varsano » Thu Jul 20, 2023 5:15 pm

Dear Zhipeng,
great you solved!

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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