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Yambo and GGA+U
Posted: Wed Jun 28, 2023 4:50 pm
by Peace
When I try to run Yambo using Quantum ESPRESSO output files with GGA+U I receive an error message containing that Hubbard U is not implemented in Yambo.
Is there a way to fix this, please?
Re: Yambo and GGA+U
Posted: Thu Jun 29, 2023 2:03 pm
by claudio
Dear Salma
it is true that is not implemented in the GW part, but you can
perform a GGA+U + BSE without problems.
The only thing you need to do is to use covariant dipoles instead of normal ones.
Namely when you calculate BSE or Optics add "-V resp" in the input file generation and set
DipApproach= "Covariant"
best
Claudio
Re: Yambo and GGA+U
Posted: Tue Jul 11, 2023 2:09 pm
by Peace
Dear Claudio,
I'm not sure how can I do that exactly. I went to my CuI.save and it contains that:
Code: Select all
X515JAB-X515JA:~/Desktop/CuI.save$ ls
charge-density.dat wfc16.dat wfc27.dat wfc38.dat wfc49.dat wfc5.dat
Cu_ONCV_PBE-1.0.UPF wfc17.dat wfc28.dat wfc39.dat wfc4.dat wfc60.dat
data-file-schema.xml wfc18.dat wfc29.dat wfc3.dat wfc50.dat wfc61.dat
I_ONCV_PBE-1.0.UPF wfc19.dat wfc2.dat wfc40.dat wfc51.dat wfc62.dat
wfc1.dat wfc30.dat wfc41.dat wfc52.dat wfc63.dat
wfc20.dat wfc31.dat wfc42.dat wfc53.dat wfc64.dat
wfc10.dat wfc21.dat wfc32.dat wfc43.dat wfc54.dat wfc6.dat
wfc11.dat wfc22.dat wfc33.dat wfc44.dat wfc55.dat wfc7.dat
wfc12.dat wfc23.dat wfc34.dat wfc45.dat wfc56.dat wfc8.dat
wfc13.dat wfc24.dat wfc35.dat wfc46.dat wfc57.dat wfc9.dat
wfc14.dat wfc25.dat wfc36.dat wfc47.dat wfc58.dat
wfc15.dat wfc26.dat wfc37.dat wfc48.dat wfc59.dat
As you can see there is not input file here where I can include what you mentioned. So I typed in terminal the command
Code: Select all
'/home/salma/Desktop/yambo-5.1.0/bin/p2y' -V resp
but I received this message in terminal
Code: Select all
/home/salma/Desktop/yambo-5.1.0/bin/p2y: unrecognized option '-V'
Can you show me step by step how can I do that please?
Re: Yambo and GGA+U
Posted: Wed Jul 12, 2023 10:11 am
by Daniele Varsano
Dear Salma,
what Claudio is suggesting is to proceed as a standard calculation:
1) p2y
2) setup yambo -i
3) Bse calculation
When doing the BSE calculation, pay attention to select the right method (covariant) to calculate the dipoles in the input file.
Best,
Daniele
Re: Yambo and GGA+U
Posted: Wed Jul 12, 2023 11:20 am
by Peace
Dear Daniele,
When I work with p2y, that's the message that I receive in terminal:
Code: Select all
salma@salma-VivoBook-ASUSLaptop-X515JAB-X515JA:~/Desktop/CuI/u/yambo/out/CuI.save$ '/home/salma/Desktop/yambo-5.1.0/bin/p2y'
_| _| _|_| _| _| _|_|_| _|_|
_| _| _| _| _|_| _|_| _| _| _| _|
_| _|_|_|_| _| _| _| _|_|_| _| _|
_| _| _| _| _| _| _| _| _|
_| _| _| _| _| _|_|_| _|_|
<---> DBs path set to : .
<---> detected QE data format : qexsd
<---> == PWscf v.6.x generated data (QEXSD fmt) ==
<---> Header/K-points/Energies... done
<---> Cell data...
<---> [WARNING]Two or more crystal structures fit the given cell done
<---> Atomic data... done
<---> Symmetries...[SI no]...[I yes]...[-I no]...[TR no]
[ERROR] LDA+U. Hubbard correction is not considered in yambo.
Re: Yambo and GGA+U
Posted: Wed Jul 12, 2023 1:19 pm
by claudio
Dear Salma
you are right, if you want to preceed with your calculation please
comment the line 870 in the file interfaces/p2y/mod_p2y.F:
if(pw_lda_plus_u) call error(' LDA+U. Hubbard correction is not considered in yambo.')
and recompile p2y, then it should work
best
Claudio
Re: Yambo and GGA+U
Posted: Wed Jul 12, 2023 4:01 pm
by Peace
Dear Claudio,
I did this:
Code: Select all
#if(pw_lda_plus_u) call error(' LDA+U. Hubbard correction is not considered in yambo.')
How can I recompile p2y, please?
Re: Yambo and GGA+U
Posted: Wed Jul 12, 2023 9:17 pm
by Daniele Varsano
Dear Salma,
comments in fortran are done with the "!" symbol.
!if(pw_lda_plus_u) call error(' LDA+U. Hubbard correction is not considered in yambo.')
Next typying:
> make interfaces
in the yambo code directory should do the job.
Best,
Daniele
Re: Yambo and GGA+U
Posted: Thu Jul 13, 2023 10:30 am
by Peace
Dear Daniele,
I received errors in the terminal after typing >make interfaces. Can you check that, please :
Code: Select all
salma@salma-VivoBook-ASUSLaptop-X515JAB-X515JA:~/Desktop/yambo-5.1.0$ make interfaces
make[4]: Nothing to be done for 'all'.
[lib/qe_pseudo] qe_pseudo (checking work to be done)
[lib/slatec] slatec (checking work to be done)
[lib/math77] math77 (checking work to be done)
[lib/local] local (checking work to be done)
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
[lib/yambo/driver/src/interface] liba2y_Ydriver_interface.a (lib)
[lib/yambo/driver/src/main] launcher
[lib/yambo/driver/src/main] input_file
[lib/yambo/driver/src/main] options_maker
[lib/yambo/driver/src/main] tool_init
[lib/yambo/driver/src/main] liba2y_Ydriver_main.a (lib)
[lib/yambo/driver/src/options] liba2y_Ydriver_options.a (lib)
[src/driver] driver (checking work to be done)
[src/tools] tools (checking work to be done)
[src/modules] modules (checking work to be done)
[src/memory] memory (checking work to be done)
[src/matrices] matrices (checking work to be done)
[src/linear_algebra] linear_algebra (checking work to be done)
[src/parallel] parallel (checking work to be done)
[src/parser] parser (checking work to be done)
[src/communicate] communicate (checking work to be done)
[src/common] common (checking work to be done)
[src/timing] timing (checking work to be done)
[src/Yio] Yio (checking work to be done)
[src/io] io (checking work to be done)
[src/setup] setup (checking work to be done)
[src/interface] interface (checking work to be done)
[src/stop_and_restart] stop_and_restart (checking work to be done)
[src/bz_ops] bz_ops (checking work to be done)
[src/driver] options_ypp
[src/driver] libdriver.a (lib)
[src/tools] libtools.a (lib)
[src/modules] mod_pars
[src/modules] mod_units
[src/modules] mod_stderr
[src/modules] mod_memory
[src/modules] mod_parallel
[src/modules] mod_com_interfcs
[src/modules] mod_electrons
[src/modules] mod_com
[src/modules] mod_cuda
[src/modules] mod_matrix_operate
[src/modules] mod_D_lattice
[src/modules] mod_descriptors
[src/modules] mod_R_lattice
[src/modules] mod_DIPOLES
[src/modules] mod_matrix
[src/modules] mod_X
[src/modules] mod_parallel_interface
[src/modules] mod_SLK
[src/modules] mod_linear_algebra
[src/modules] mod_wrapper
[src/modules] mod_wrapper_omp
[src/modules] mod_FFT
[src/modules] mod_LIVE_t
[src/modules] mod_logo
[src/modules] mod_cutoff_ws
[src/modules] mod_timing
[src/modules] mod_wave_func
[src/modules] mod_xc_functionals
[src/modules] mod_global_XC
[src/modules] mod_frequency
[src/modules] mod_vec_operate
[src/modules] mod_functions
[src/modules] mod_zeros
[src/modules] mod_atom_proj
[src/modules] mod_pseudo
[src/modules] mod_QP
[src/modules] mod_collision_el
[src/modules] mod_BS
[src/modules] mod_BS_solvers
[src/modules] mod_QP_CTL
[src/modules] mod_TDDFT
[src/modules] mod_ACFDT
[src/modules] mod_MAGNONS
[src/modules] mod_DICHROISM
[src/modules] mod_PHOTOLUM
[src/modules] mod_IO_interfaces
[src/modules] mod_IO
[src/modules] mod_ELPH
[src/modules] mod_PHEL
[src/modules] mod_interfaces
[src/modules] mod_X_output
[src/modules] mod_OUTPUT_simple
[src/modules] mod_POL_FIT
[src/modules] mod_RT_lifetimes
[src/modules] mod_RT_occupations
[src/modules] mod_real_time
[src/modules] mod_hamiltonian
[src/modules] mod_debug
[src/modules] mod_interpolate
[src/modules] mod_interpolate_tools
[src/modules] SET_logicals
[src/modules] mod_RT_control
[src/modules] mod_RT_output
[src/modules] mod_SC
[src/modules] mod_collision_ext
[src/modules] mod_electric
[src/modules] mod_fields
[src/modules] mod_magnetic
[src/modules] mod_nl_optics
[src/modules] mod_plasma
[src/modules] SET_defaults
[src/modules] libmodules.a (lib)
[src/memory] libmemory.a (lib)
[src/matrices] libmatrices.a (lib)
[src/linear_algebra] SERIAL_HERMITIAN_diagonalization
[src/linear_algebra] SERIAL_lin_system
[src/linear_algebra] liblinear_algebra.a (lib)
[src/parallel] PARALLEL_global_reset
[src/parallel] PARALLEL_global_dimensions
[src/parallel] PARALLEL_global_Self_Energy
[src/parallel] PARALLEL_global_indexes
[src/parallel] PARALLEL_WF_distribute
[src/parallel] libparallel.a (lib)
[src/parser] libparser.a (lib)
[src/communicate] libcommunicate.a (lib)
[src/common] OCCUPATIONS_Gaps
[src/common] libcommon.a (lib)
[src/timing] libtiming.a (lib)
[src/Yio] libYio.a (lib)
[src/io] io_DB1
[src/io] io_DIPOLES_PAR
[src/io] libio.a (lib)
[src/setup] PARALLEL_and_IO_Setup
make[2]: *** [/home/salma/Desktop/yambo-5.1.0/config/mk/local/rules.mk:9: QP_state_table_setup.o] Error 1
make[1]: *** [config/mk/global/actions/compile_interfaces.mk:26: a2y] Error 2
make[4]: Nothing to be done for 'all'.
[lib/qe_pseudo] qe_pseudo (checking work to be done)
[lib/slatec] slatec (checking work to be done)
[lib/math77] math77 (checking work to be done)
[lib/local] local (checking work to be done)
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
[lib/yambo/driver/src/interface] libc2y_Ydriver_interface.a (lib)
[lib/yambo/driver/src/main] launcher
[lib/yambo/driver/src/main] options_maker
[lib/yambo/driver/src/main] tool_init
[lib/yambo/driver/src/main] libc2y_Ydriver_main.a (lib)
[lib/yambo/driver/src/options] libc2y_Ydriver_options.a (lib)
[src/driver] driver (checking work to be done)
[src/tools] tools (checking work to be done)
[src/modules] modules (checking work to be done)
[src/memory] memory (checking work to be done)
[src/matrices] matrices (checking work to be done)
[src/linear_algebra] linear_algebra (checking work to be done)
[src/parallel] parallel (checking work to be done)
[src/parser] parser (checking work to be done)
[src/communicate] communicate (checking work to be done)
[src/common] common (checking work to be done)
[src/timing] timing (checking work to be done)
[src/Yio] Yio (checking work to be done)
[src/io] io (checking work to be done)
[src/setup] setup (checking work to be done)
[src/interface] interface (checking work to be done)
[src/stop_and_restart] stop_and_restart (checking work to be done)
[src/bz_ops] bz_ops (checking work to be done)
make[2]: *** [/home/salma/Desktop/yambo-5.1.0/config/mk/local/rules.mk:9: QP_state_table_setup.o] Error 1
make[1]: *** [config/mk/global/actions/compile_interfaces.mk:26: c2y] Error 2
make[4]: Nothing to be done for 'all'.
[lib/qe_pseudo] qe_pseudo (checking work to be done)
[lib/slatec] slatec (checking work to be done)
[lib/math77] math77 (checking work to be done)
[lib/local] local (checking work to be done)
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
[lib/yambo/driver/src/interface] libp2y_Ydriver_interface.a (lib)
[lib/yambo/driver/src/main] launcher
[lib/yambo/driver/src/main] options_maker
[lib/yambo/driver/src/main] tool_init
[lib/yambo/driver/src/main] libp2y_Ydriver_main.a (lib)
[lib/yambo/driver/src/options] libp2y_Ydriver_options.a (lib)
[src/driver] driver (checking work to be done)
[src/tools] tools (checking work to be done)
[src/modules] modules (checking work to be done)
[src/memory] memory (checking work to be done)
[src/matrices] matrices (checking work to be done)
[src/linear_algebra] linear_algebra (checking work to be done)
[src/parallel] parallel (checking work to be done)
[src/parser] parser (checking work to be done)
[src/communicate] communicate (checking work to be done)
[src/common] common (checking work to be done)
[src/timing] timing (checking work to be done)
[src/Yio] Yio (checking work to be done)
[src/io] io (checking work to be done)
[src/setup] setup (checking work to be done)
[src/interface] interface (checking work to be done)
[src/stop_and_restart] stop_and_restart (checking work to be done)
[src/bz_ops] bz_ops (checking work to be done)
[src/driver] libdriver.a (lib)
[src/tools] libtools.a (lib)
[src/modules] libmodules.a (lib)
[src/memory] libmemory.a (lib)
[src/matrices] libmatrices.a (lib)
[src/linear_algebra] liblinear_algebra.a (lib)
[src/parallel] libparallel.a (lib)
[src/parser] libparser.a (lib)
[src/communicate] libcommunicate.a (lib)
[src/common] libcommon.a (lib)
[src/timing] libtiming.a (lib)
[src/Yio] libYio.a (lib)
[src/io] libio.a (lib)
make[2]: *** [/home/salma/Desktop/yambo-5.1.0/config/mk/local/rules.mk:9: QP_state_table_setup.o] Error 1
make[1]: *** [config/mk/global/actions/compile_interfaces.mk:26: p2y] Error 2
I also checked if p2y works but I receive always the same error :
Code: Select all
[ERROR] LDA+U. Hubbard correction is not considered in yambo.
Re: Yambo and GGA+U
Posted: Wed Jul 19, 2023 1:46 pm
by claudio
Dear Salma
please post the log files of the compilation that are in the log/ folder
in such a way we can have a look to the error
best
Claudio