Re: [Pw_forum] errors testing espresso 5.4.0

[Paolo Giannozzi]

Well, no, the array that goes out of bounds serves some purpose: it
contains an additional potential term. 100% guaranteed bug. It affects only
the case of Tkatchenko-Scheffler correction for van der Waals forces (also
in CP) though.

Paolo

On Mon, Sep 5, 2016 at 7:17 AM, Paolo Giannozzi 
wrote:

> These are out-of-bounds errors: the code is trying to access a
> non-existing array element. This kind of errors is serious and must not be
> present. In the specific case: the first two errors are harmless, since the
> out-of-bound element is not assigned a value or used in calculations. The
> third seems more serious. Apparently the array that goes out of bounds
> serves no purpose, but I don't know much about that part of the code. Thank
> you for reporting this.
>
> Paolo
>
> On Sat, Sep 3, 2016 at 2:50 AM, Fabricio Cannini 
> wrote:
>
>> Hello there
>>
>> I'm facing errors in a few tests of espresso 5.4.0.
>> I'm compiling it a centos 6.x machine in the following manner:
>> =
>> FC = intel 15.0
>> MPI = impi 5.0
>> BLAS/LAPACK = mkl 11.2
>> FFT = fftw 3.3.5
>>
>> BLAS_LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
>> LAPACK_LIBS="-lmkl_core"
>> FFT_LIBS="-lfftw3"
>> FFLAGS="-O2 -assume byterecl -g -traceback -fpe0 -CB -openmp"
>> MPIF90=mpiifort
>>
>> ./configure --enable-openmp --enable-parallel --without-scalapack
>>
>> make pw cp ph neb epw
>> =
>>
>>
>> When running the pw tests, some of those fail no matter how many mpi
>> processes I use.
>>
>> 'pw_b3lyp/b3lyp-h2o.in' and 'pw_b3lyp/b3lyp-O.in' fail with the error
>> message:
>> ---
>> forrtl: severe (408): fort: (2): Subscript #1 of the array CORR has
>> value 12 which is greater than the upper bound of 10
>>
>> Image  PCRoutineLine
>> Source
>> pw.x   016F0EF0  Unknown   Unknown
>> Unknown
>> pw.x   00D7B085  funct_mp_set_dft_ 597
>> funct.f90
>> pw.x   00D79837  funct_mp_enforce_ 723
>> funct.f90
>> pw.x   00E2E054  read_pseudo_mod_m 101
>> read_pseudo.f90
>> pw.x   006EA301  iosys_   1444
>> input.f90
>> pw.x   004080B9  run_pwscf_ 63
>> run_pwscf.f90
>> pw.x   00407FBD  MAIN__ 30
>> pwscf.f90
>> pw.x   00407F1E  Unknown   Unknown
>> Unknown
>> libc.so.6  0034F221ED1D  Unknown   Unknown
>> Unknown
>> pw.x   00407E29  Unknown   Unknown
>> Unknown
>> ---
>>
>>
>> 'pw_uspp/uspp-hyb-g.in' fails with the error message:
>> ---
>> forrtl: severe (408): fort: (2): Subscript #1 of the array DSPHER has
>> value 1 which is greater than the upper bound of 0
>>
>> Image  PCRoutineLine
>> Source
>> pw.x   016F0EF0  Unknown   Unknown
>> Unknown
>> pw.x   00517B8C  realus_mp_real_sp 602
>> realus.f90
>> pw.x   0050D056  realus_mp_addusfo1284
>> realus.f90
>> pw.x   00AFB1F6  force_us_.L   113
>> force_us.f90
>> pw.x   006A3415  forces_90
>> forces.f90
>> pw.x   004081B8  run_pwscf_129
>> run_pwscf.f90
>> pw.x   00407FBD  MAIN__ 30
>> pwscf.f90
>> pw.x   00407F1E  Unknown   Unknown
>> Unknown
>> libc.so.6  0034F221ED1D  Unknown   Unknown
>> Unknown
>> pw.x   00407E29  Unknown   Unknown
>> Unknown
>> ---
>>
>>
>> 'pw_vdw/vdw-ts.in' fails with the error message:
>> ---
>> forrtl: severe (408): fort: (2): Subscript #1 of the array UTSVDW has
>> value 5201 which is greater than the upper bound of 5200
>>
>> Image  PCRoutineLine
>> Source
>> pw.x   016F0EF0  Unknown   Unknown
>> Unknown
>> pw.x   00470436  v_of_rho_  92
>> v_of_rho.f90
>> pw.x   0080AE0B  potinit_  227
>> potinit.f90
>> pw.x   006D98F8  init_run_  99
>> init_run.f90
>> pw.x   00408111  run_pwscf_ 78
>> run_pwscf.f90
>> pw.x   00407FBD  MAIN__ 30
>> pwscf.f90
>> pw.x   00407F1E  Unknown   Unknown
>> Unknown
>> libc.so.6  0034F221ED1D  Unknown   Unknown
>> Unknown
>> pw.x   

Re: [Pw_forum] errors testing espresso 5.4.0

[Paolo Giannozzi]

These are out-of-bounds errors: the code is trying to access a non-existing
array element. This kind of errors is serious and must not be present. In
the specific case: the first two errors are harmless, since the
out-of-bound element is not assigned a value or used in calculations. The
third seems more serious. Apparently the array that goes out of bounds
serves no purpose, but I don't know much about that part of the code. Thank
you for reporting this.

Paolo

On Sat, Sep 3, 2016 at 2:50 AM, Fabricio Cannini  wrote:

> Hello there
>
> I'm facing errors in a few tests of espresso 5.4.0.
> I'm compiling it a centos 6.x machine in the following manner:
> =
> FC = intel 15.0
> MPI = impi 5.0
> BLAS/LAPACK = mkl 11.2
> FFT = fftw 3.3.5
>
> BLAS_LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
> LAPACK_LIBS="-lmkl_core"
> FFT_LIBS="-lfftw3"
> FFLAGS="-O2 -assume byterecl -g -traceback -fpe0 -CB -openmp"
> MPIF90=mpiifort
>
> ./configure --enable-openmp --enable-parallel --without-scalapack
>
> make pw cp ph neb epw
> =
>
>
> When running the pw tests, some of those fail no matter how many mpi
> processes I use.
>
> 'pw_b3lyp/b3lyp-h2o.in' and 'pw_b3lyp/b3lyp-O.in' fail with the error
> message:
> ---
> forrtl: severe (408): fort: (2): Subscript #1 of the array CORR has
> value 12 which is greater than the upper bound of 10
>
> Image  PCRoutineLine
> Source
> pw.x   016F0EF0  Unknown   Unknown  Unknown
> pw.x   00D7B085  funct_mp_set_dft_ 597
> funct.f90
> pw.x   00D79837  funct_mp_enforce_ 723
> funct.f90
> pw.x   00E2E054  read_pseudo_mod_m 101
> read_pseudo.f90
> pw.x   006EA301  iosys_   1444
> input.f90
> pw.x   004080B9  run_pwscf_ 63
> run_pwscf.f90
> pw.x   00407FBD  MAIN__ 30
> pwscf.f90
> pw.x   00407F1E  Unknown   Unknown  Unknown
> libc.so.6  0034F221ED1D  Unknown   Unknown  Unknown
> pw.x   00407E29  Unknown   Unknown  Unknown
> ---
>
>
> 'pw_uspp/uspp-hyb-g.in' fails with the error message:
> ---
> forrtl: severe (408): fort: (2): Subscript #1 of the array DSPHER has
> value 1 which is greater than the upper bound of 0
>
> Image  PCRoutineLine
> Source
> pw.x   016F0EF0  Unknown   Unknown  Unknown
> pw.x   00517B8C  realus_mp_real_sp 602
> realus.f90
> pw.x   0050D056  realus_mp_addusfo1284
> realus.f90
> pw.x   00AFB1F6  force_us_.L   113
> force_us.f90
> pw.x   006A3415  forces_90
> forces.f90
> pw.x   004081B8  run_pwscf_129
> run_pwscf.f90
> pw.x   00407FBD  MAIN__ 30
> pwscf.f90
> pw.x   00407F1E  Unknown   Unknown  Unknown
> libc.so.6  0034F221ED1D  Unknown   Unknown  Unknown
> pw.x   00407E29  Unknown   Unknown  Unknown
> ---
>
>
> 'pw_vdw/vdw-ts.in' fails with the error message:
> ---
> forrtl: severe (408): fort: (2): Subscript #1 of the array UTSVDW has
> value 5201 which is greater than the upper bound of 5200
>
> Image  PCRoutineLine
> Source
> pw.x   016F0EF0  Unknown   Unknown  Unknown
> pw.x   00470436  v_of_rho_  92
> v_of_rho.f90
> pw.x   0080AE0B  potinit_  227
> potinit.f90
> pw.x   006D98F8  init_run_  99
> init_run.f90
> pw.x   00408111  run_pwscf_ 78
> run_pwscf.f90
> pw.x   00407FBD  MAIN__ 30
> pwscf.f90
> pw.x   00407F1E  Unknown   Unknown  Unknown
> libc.so.6  0034F221ED1D  Unknown   Unknown  Unknown
> pw.x   00407E29  Unknown   Unknown  Unknown
> ---
>
>
>
> All messages are similar so they may have a common cause, but I'm unable
> to tell why exactly. Any ideas?
>
>
> TIA,
> Fabricio
> ___
> Pw_forum mailing list
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> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 

Re: [Pw_forum] lda+U abinitio U

[Matteo Cococcioni]

Hi Lorenzo,

the two tutorial should be quite equivalent, although the one Federico
found is more recent and probably I updated some details.

Regarding your questions: as far as I understand you are only interested in
U on one specific atomic species of your materials. You could do that by
doing two perturbations: one on the atom you are interested in, the second
on all the other atoms (which you treat as a "macro-atom") at the same
time. Of course the occupation of this second "extended atom" is the sum of
the occupations of the atoms it is composed by. you then construct a 2x2
response matrix that, once inverted, should give you the U you are looking
for (throwing away the one for the "macro-atom").
This only limits the number of perturbation but still requires a supercell
of sufficiently large size.

We are working on a way to make the whole procedure more efficient, through
automatizing the linear-response, but the code is not ready yet.

Best,

Matteo

On Fri, Sep 2, 2016 at 5:55 PM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

> Hello,
> I have a question about how to compute the abinitio U, I'm following the
> online Santa Barbara 2009 tutorial (and trying to use the script therein)
> and
> PRB 71, 35105 (2005).
>
> I have a system that is not very large but quite heavy to compute, and have
> several atomic species (3 at first, then 4) but only one is problematic,
> as it
> is could be Cerium or other Lanthanoids.
>
> It would be quite anoying and very cpu time consuming for me to properly*
> compute U by finite response for all the species, but I'm not sure that
> 1. it is possible with the available toolchain
> 2. it makes sense
>
> Also, if somebody (e.g. Matteo) has some more recent and/or more user
> friendly
> code to compute dalpha/dn I'm a taker.
>
> thank you for your help!
>
> *) by properly I mean take care that it is converged with the supercell
> size
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> +33 (0)1 44 275 084 / skype: paulatz
> http://www.impmc.upmc.fr/~paulatto/
> 23-24/4é16 Boîte courrier 115,
> 4 place Jussieu 75252 Paris Cédex 05
>
> ___
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> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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Re: [Pw_forum] About using plotproj.x

[Abdullah N. Albarakati]

Dear QE experts,

Thank you very much for your consideration,

Dear Sterfano
Thank you very much,
I did what you explain, but the code ask for other information.

what is threshold?
what is ncri?

Best wishes,

Abdullah


From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of 
stefano de gironcoli [degir...@sissa.it]
Sent: Sunday, September 04, 2016 12:54 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] About using plotproj.x

Dear Abdullah,
The first is a file with the band eigenvalues, written in the output of pw.x.
 just take the output of pw.x the one used to produce the projection and cut 
out the eivenvaulues section adding nbnd and nks on top

The second file is written by the projwfc.x program with the option lsym=.false.
should be the file corresponding to filproj in projwfc.x namelist

stefano




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Re: [Pw_forum] errors testing espresso 5.4.0

[Filippo SPIGA]

Dear Fabricio,

are you running these tests manually or via test-suite?

Well, the error messages are quite clear so it is a matter of investigate if 
these are repsoducible. We are tracking bugs in a very "amateurial way" at the 
moment but we will look into it.

Thanks for reporting 

On Sep 3, 2016, at 1:50 AM, Fabricio Cannini  wrote:
> Hello there
> 
> I'm facing errors in a few tests of espresso 5.4.0.
> I'm compiling it a centos 6.x machine in the following manner:
> =
> FC = intel 15.0
> MPI = impi 5.0
> BLAS/LAPACK = mkl 11.2
> FFT = fftw 3.3.5
> 
> BLAS_LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
> LAPACK_LIBS="-lmkl_core"
> FFT_LIBS="-lfftw3"
> FFLAGS="-O2 -assume byterecl -g -traceback -fpe0 -CB -openmp"
> MPIF90=mpiifort
> 
> ./configure --enable-openmp --enable-parallel --without-scalapack
> 
> make pw cp ph neb epw
> =
> 
> 
> When running the pw tests, some of those fail no matter how many mpi 
> processes I use.
> 
> 'pw_b3lyp/b3lyp-h2o.in' and 'pw_b3lyp/b3lyp-O.in' fail with the error 
> message:
> ---
> forrtl: severe (408): fort: (2): Subscript #1 of the array CORR has 
> value 12 which is greater than the upper bound of 10
> 
> Image  PCRoutineLine 
> Source
> pw.x   016F0EF0  Unknown   Unknown  Unknown
> pw.x   00D7B085  funct_mp_set_dft_ 597 
> funct.f90
> pw.x   00D79837  funct_mp_enforce_ 723 
> funct.f90
> pw.x   00E2E054  read_pseudo_mod_m 101 
> read_pseudo.f90
> pw.x   006EA301  iosys_   1444 
> input.f90
> pw.x   004080B9  run_pwscf_ 63 
> run_pwscf.f90
> pw.x   00407FBD  MAIN__ 30 
> pwscf.f90
> pw.x   00407F1E  Unknown   Unknown  Unknown
> libc.so.6  0034F221ED1D  Unknown   Unknown  Unknown
> pw.x   00407E29  Unknown   Unknown  Unknown
> ---
> 
> 
> 'pw_uspp/uspp-hyb-g.in' fails with the error message:
> ---
> forrtl: severe (408): fort: (2): Subscript #1 of the array DSPHER has 
> value 1 which is greater than the upper bound of 0
> 
> Image  PCRoutineLine 
> Source
> pw.x   016F0EF0  Unknown   Unknown  Unknown
> pw.x   00517B8C  realus_mp_real_sp 602 
> realus.f90
> pw.x   0050D056  realus_mp_addusfo1284 
> realus.f90
> pw.x   00AFB1F6  force_us_.L   113 
> force_us.f90
> pw.x   006A3415  forces_90 
> forces.f90
> pw.x   004081B8  run_pwscf_129 
> run_pwscf.f90
> pw.x   00407FBD  MAIN__ 30 
> pwscf.f90
> pw.x   00407F1E  Unknown   Unknown  Unknown
> libc.so.6  0034F221ED1D  Unknown   Unknown  Unknown
> pw.x   00407E29  Unknown   Unknown  Unknown
> ---
> 
> 
> 'pw_vdw/vdw-ts.in' fails with the error message:
> ---
> forrtl: severe (408): fort: (2): Subscript #1 of the array UTSVDW has 
> value 5201 which is greater than the upper bound of 5200
> 
> Image  PCRoutineLine 
> Source
> pw.x   016F0EF0  Unknown   Unknown  Unknown
> pw.x   00470436  v_of_rho_  92 
> v_of_rho.f90
> pw.x   0080AE0B  potinit_  227 
> potinit.f90
> pw.x   006D98F8  init_run_  99 
> init_run.f90
> pw.x   00408111  run_pwscf_ 78 
> run_pwscf.f90
> pw.x   00407FBD  MAIN__ 30 
> pwscf.f90
> pw.x   00407F1E  Unknown   Unknown  Unknown
> libc.so.6  0034F221ED1D  Unknown   Unknown  Unknown
> pw.x   00407E29  Unknown   Unknown  Unknown
> ---
> 
> 
> 
> All messages are similar so they may have a common cause, but I'm unable 
> to tell why exactly. Any ideas?
> 
> 
> TIA,
> Fabricio
> ___
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--
Filippo SPIGA ~ Quantum ESPRESSO Foundation ~ http://www.quantum-espresso.org


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Re: [Pw_forum] About using plotproj.x

[stefano de gironcoli]

Dear Abdullah,
The first is a file with the band eigenvalues, written in the output of 
pw.x.
 just take the output of pw.x the one used to produce the projection 
and cut out the eivenvaulues section adding nbnd and nks on top


The second file is written by the projwfc.x program with the option 
lsym=.false.

should be the file corresponding to filproj in projwfc.x namelist

stefano

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Re: [Pw_forum] lda+U abinitio U

[Federico Iori]

Hi. 
I found this online... 

http://www.iiserpune.ac.in/~smr2626/hands_on/week1/july4/ 

could it help? 



Federico IORI 
Marie Curie Fellow 
Laboratoire de Physique des Solides 
Bâtiment 510 - Rue André Rivière 
91400 Orsay 


- Mensaje original -

De: "Lorenzo Paulatto"  
Para: "pw forum"  
Enviados: Viernes, 2 de Septiembre 2016 17:55:55 
Asunto: [Pw_forum] lda+U abinitio U 

Hello, 
I have a question about how to compute the abinitio U, I'm following the 
online Santa Barbara 2009 tutorial (and trying to use the script therein) and 
PRB 71, 35105 (2005). 

I have a system that is not very large but quite heavy to compute, and have 
several atomic species (3 at first, then 4) but only one is problematic, as it 
is could be Cerium or other Lanthanoids. 

It would be quite anoying and very cpu time consuming for me to properly* 
compute U by finite response for all the species, but I'm not sure that 
1. it is possible with the available toolchain 
2. it makes sense 

Also, if somebody (e.g. Matteo) has some more recent and/or more user friendly 
code to compute dalpha/dn I'm a taker. 

thank you for your help! 

*) by properly I mean take care that it is converged with the supercell size 

-- 
Dr. Lorenzo Paulatto 
IdR @ IMPMC -- CNRS & Université Paris 6 
+33 (0)1 44 275 084 / skype: paulatz 
http://www.impmc.upmc.fr/~paulatto/ 
23-24/4é16 Boîte courrier 115, 
4 place Jussieu 75252 Paris Cédex 05 

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