[QE-users] qe-6.4.1-qmcpack vs qe-6.7 Performace?

2021-02-15 Thread Stephen Zhang
Hi Everyone,

I'm currently using both the latest qe-6.7 and qe-6.4.1 qmcpack in my
school computing HPC cluster and i've noticed that qe-6.4.1-qmcpack's
version of pw.x is several times faster than qe-6.7 when performing scf and
nscf runs. Both were configured for parallel runs using openmpi. Another
difference is that while qe-6.4.1-qmcpack's pw.x is much faster during the
run, it is also much slower when writing the data into prefix.save compared
to qe-6.7, however this may be due to the fact that the 6.4.1-qmcpack's
pw.x is configured to write the wavefunctions in the hdf5 format. The final
difference I noticed was that qe-6.4.1-qmcpack's pw.x's filesize is much
larger at 20mb compared to 4mb for qe-6.7's pw.x.

Thanks,
Stephen


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Re: [QE-users] Error in routine cdiaghg (1): problems computing cholesky

2021-02-15 Thread Robert Stanton
Hello Bhumika,

 This cholesky issue can happen when the input geometry is problematic.
I believe in your case you have some atoms overlapping in the periodic
images. You can double check this with a GUI/visualizer if needed, or use
the materialscloud resource to generate input directly from your geometry
file. Hope this helps.

Regards,
Robert Stanton
Graduate Student
Clarkson University

On Mon, Feb 15, 2021 at 12:07 PM Bhumika Longakshi <
longakshi_bhum...@iitgn.ac.in> wrote:

> Dear All,
>
> I have been trying to do BOMD simulation but it is giving me an error
> message: Error in routine cdiaghg (1): problems computing cholesky
>
> Below is the input script and the output message. Can you please help me
> with this?
>
> 
> calculation = 'relax'
> prefix = 'ni'
> outdir='./outdir'
> pseudo_dir = '/home/grp/1/pseudo/'
> etot_conv_thr = 1e-6
> forc_conv_thr = 1e-5
> /
> 
> ibrav=2,
> a=7.01159, b=7.01159, c=10.51739,
> nat=48, ntyp=1,
> ecutwfc=75, ecutrho =  476
> occupations='smearing', smearing='gaussian', degauss=0.01
> nspin=2
> starting_magnetization(1)=0.1
> /
> 
> conv_thr=1e-8
> /
> 
> ion_dynamics='bfgs'
> /
> 
> cell_dofree='ibrav'
> /
> ATOMIC_SPECIES
>  Ni 58.6934 Ni.pbe-spn-kjpaw_psl.1.0.0.UPF
> ATOMIC_POSITIONS (alat)
>  Ni0.0 0.0 0.0
>  Ni0.0 0.0 3.505798126
>  Ni0.0 0.0 7.011596253
>  Ni0.0 3.505798101 0.0
>  Ni0.0 3.505798101 3.505798126
>  Ni0.0 3.505798101 7.011596253
>  Ni3.505798101 0.0 0.0
>  Ni3.505798101 0.0 3.505798126
>  Ni3.505798101 0.0 7.011596253
>  Ni3.505798101 3.505798101 0.0
>  Ni3.505798101 3.505798101 3.505798126
>  Ni3.505798101 3.505798101 7.011596253
>  Ni0.0 1.752899051 1.752899063
>  Ni0.0 1.752899051 5.258697033
>  Ni0.0 1.752899051 8.764494846
>  Ni0.0 5.258697152 1.752899063
>  Ni0.0 5.258697152 5.258697033
>  Ni0.0 5.258697152 8.764494846
>  Ni3.505798101 1.752899051 1.752899063
>  Ni3.505798101 1.752899051 5.258697033
>  Ni3.505798101 1.752899051 8.764494846
>  Ni3.505798101 5.258697152 1.752899063
>  Ni3.505798101 5.258697152 5.258697033
>  Ni3.505798101 5.258697152 8.764494846
>  Ni1.752899051 0.0 1.752899063
>  Ni1.752899051 0.0 5.258697033
>  Ni1.752899051 0.0 8.764494846
>  Ni1.752899051 3.505798101 1.752899063
>  Ni1.752899051 3.505798101 5.258697033
>  Ni1.752899051 3.505798101 8.764494846
>  Ni5.258697152 0.0 1.752899063
>  Ni5.258697152 0.0 5.258697033
>  Ni5.258697152 0.0 8.764494846
>  Ni5.258697152 3.505798101 1.752899063
>  Ni5.258697152 3.505798101 5.258697033
>  Ni5.258697152 3.505798101 8.764494846
>  Ni1.752899051 1.752899051 0.0
>  Ni1.752899051 1.752899051 3.505798126
>  Ni1.752899051 1.752899051 7.011596253
>  Ni1.752899051 5.258697152 0.0
>  Ni1.752899051 5.258697152 3.505798126
>  Ni1.752899051 5.258697152 7.011596253
>  Ni5.258697152 1.752899051 0.0
>  Ni5.258697152 1.752899051 3.505798126
>  Ni5.258697152 1.752899051 7.011596253
>  Ni5.258697152 5.258697152 0.0
>  Ni5.258697152 5.258697152 3.505798126
>  Ni5.258697152 5.258697152 7.011596253
>
> K_POINTS (automatic)
>   1 1 1 0 0 0
>
>
> %%
>  Error in routine  cdiaghg (1):
>   problems computing cholesky
>
>  
> %%
>
> Thank You.
>
> Regards,
> Bhumika Longakshi
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> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
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[QE-users] Error in routine cdiaghg (1): problems computing cholesky

2021-02-15 Thread Bhumika Longakshi
Dear All,

I have been trying to do BOMD simulation but it is giving me an error
message: Error in routine cdiaghg (1): problems computing cholesky

Below is the input script and the output message. Can you please help me
with this?


calculation = 'relax'
prefix = 'ni'
outdir='./outdir'
pseudo_dir = '/home/grp/1/pseudo/'
etot_conv_thr = 1e-6
forc_conv_thr = 1e-5
/

ibrav=2,
a=7.01159, b=7.01159, c=10.51739,
nat=48, ntyp=1,
ecutwfc=75, ecutrho =  476
occupations='smearing', smearing='gaussian', degauss=0.01
nspin=2
starting_magnetization(1)=0.1
/

conv_thr=1e-8
/

ion_dynamics='bfgs'
/

cell_dofree='ibrav'
/
ATOMIC_SPECIES
 Ni 58.6934 Ni.pbe-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (alat)
 Ni0.0 0.0 0.0
 Ni0.0 0.0 3.505798126
 Ni0.0 0.0 7.011596253
 Ni0.0 3.505798101 0.0
 Ni0.0 3.505798101 3.505798126
 Ni0.0 3.505798101 7.011596253
 Ni3.505798101 0.0 0.0
 Ni3.505798101 0.0 3.505798126
 Ni3.505798101 0.0 7.011596253
 Ni3.505798101 3.505798101 0.0
 Ni3.505798101 3.505798101 3.505798126
 Ni3.505798101 3.505798101 7.011596253
 Ni0.0 1.752899051 1.752899063
 Ni0.0 1.752899051 5.258697033
 Ni0.0 1.752899051 8.764494846
 Ni0.0 5.258697152 1.752899063
 Ni0.0 5.258697152 5.258697033
 Ni0.0 5.258697152 8.764494846
 Ni3.505798101 1.752899051 1.752899063
 Ni3.505798101 1.752899051 5.258697033
 Ni3.505798101 1.752899051 8.764494846
 Ni3.505798101 5.258697152 1.752899063
 Ni3.505798101 5.258697152 5.258697033
 Ni3.505798101 5.258697152 8.764494846
 Ni1.752899051 0.0 1.752899063
 Ni1.752899051 0.0 5.258697033
 Ni1.752899051 0.0 8.764494846
 Ni1.752899051 3.505798101 1.752899063
 Ni1.752899051 3.505798101 5.258697033
 Ni1.752899051 3.505798101 8.764494846
 Ni5.258697152 0.0 1.752899063
 Ni5.258697152 0.0 5.258697033
 Ni5.258697152 0.0 8.764494846
 Ni5.258697152 3.505798101 1.752899063
 Ni5.258697152 3.505798101 5.258697033
 Ni5.258697152 3.505798101 8.764494846
 Ni1.752899051 1.752899051 0.0
 Ni1.752899051 1.752899051 3.505798126
 Ni1.752899051 1.752899051 7.011596253
 Ni1.752899051 5.258697152 0.0
 Ni1.752899051 5.258697152 3.505798126
 Ni1.752899051 5.258697152 7.011596253
 Ni5.258697152 1.752899051 0.0
 Ni5.258697152 1.752899051 3.505798126
 Ni5.258697152 1.752899051 7.011596253
 Ni5.258697152 5.258697152 0.0
 Ni5.258697152 5.258697152 3.505798126
 Ni5.258697152 5.258697152 7.011596253

K_POINTS (automatic)
  1 1 1 0 0 0

%%
 Error in routine  cdiaghg (1):
  problems computing cholesky
 %%

Thank You.

Regards,
Bhumika Longakshi
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Re: [QE-users] Fwd: error with qe 6.5

2021-02-15 Thread José Carlos Conesa Cegarra

Dear all,

Indeed I mistakedly confounded the conv_thr and ecutwfc values. Looking 
at the instructions I see now that ecutwfc is a value in Rydbergs. One 
reason for my mistake is that the ecutwfc values suggested for Co and Sn 
in the pseudos I used are 0.00 Ry; I did not go further, if I had looked 
for the pseudos of Ge and N I would have seen that the suggested values 
are around 40 Ry.


I will change the ecutwfc values to an average of those given by 
Giuseppe, and might test a few others.


Thanks to all,

José C. Conesa

El 15/02/2021 a las 12:46, Giuseppe Mattioli escribió:


Dear José

Maybe you are mistaking ecutwfc (in namelist ) with conv_thr 
(in namelist ). The former is the wavefunction cutoff (in 
Ry). Its generally meaningful values, depending on pseudopotential 
type, are in a 25~250 Ry range. Thus your 1.0D-8 value is absurdly 
small. The latter is the convergence threshold for wavefunctions in 
the iterative scf steps. Its default value is 1.0D-6 and may be 
lowered down to 1.0D-10 for different kinds of general-purpose 
calculation.


Without seeing sssp convergence tests, I would expect for your 
pseudopotentials values around


ecutwfc=40~60 Ry
ecutrho=320~600 Ry

HTH
Giuseppe

Quoting José Carlos Conesa Cegarra :


I mean,

ecutwfc=1.0D-8

JC Conesa

El 14/02/2021 a las 20:38, Paolo Giannozzi escribió:

"decreasing" ?

On Sun, Feb 14, 2021 at 8:16 PM José Carlos Conesa Cegarra 
mailto:jccon...@icp.csic.es>> wrote:


   Dear all,

   Even decreasing ecutwfc by two orders of magnitude the error
   remains the same. The PBE pseudopotentials are those included in

   https://www.materialscloud.org/discover/sssp/table/
   

   Please help.

    Mensaje reenviado 
   Asunto: [QE-users] error with qe 6.5
   Fecha: Fri, 12 Feb 2021 13:49:24 +0100
   De: José Carlos Conesa Cegarra 
   
   Responder a: Quantum ESPRESSO users Forum
   
   
   Para: Quantum ESPRESSO users Forum
   
   



   Dear all,

   I have found (several times) this error with qe-6.5:

 %%
    Error in routine allocate_fft (1):
    wrong ngm
 %%

    stopping ...

   The input file is attached. Please help

   -- José C. Conesa
   Research Professor
   Instituto de Catálisis y Petroleoquímica, CSIC
   Marie Curie, 2; Campus de Cantoblanco
   28028 Madrid (Spain)
   Phone +34 915854766



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   )
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


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--
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Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie, 2; Campus de Cantoblanco
28028 Madrid (Spain)
Phone +34 915854766




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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--
José C. Conesa
Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie, 2; Campus de Cantoblanco
28028 Madrid (Spain)
Phone +34 915854766


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Re: [QE-users] Fwd: error with qe 6.5

2021-02-15 Thread Giuseppe Mattioli


Dear José

Maybe you are mistaking ecutwfc (in namelist ) with conv_thr  
(in namelist ). The former is the wavefunction cutoff (in  
Ry). Its generally meaningful values, depending on pseudopotential  
type, are in a 25~250 Ry range. Thus your 1.0D-8 value is absurdly  
small. The latter is the convergence threshold for wavefunctions in  
the iterative scf steps. Its default value is 1.0D-6 and may be  
lowered down to 1.0D-10 for different kinds of general-purpose  
calculation.


Without seeing sssp convergence tests, I would expect for your  
pseudopotentials values around


ecutwfc=40~60 Ry
ecutrho=320~600 Ry

HTH
Giuseppe

Quoting José Carlos Conesa Cegarra :


I mean,

ecutwfc=1.0D-8

JC Conesa

El 14/02/2021 a las 20:38, Paolo Giannozzi escribió:

"decreasing" ?

On Sun, Feb 14, 2021 at 8:16 PM José Carlos Conesa Cegarra  
mailto:jccon...@icp.csic.es>> wrote:


   Dear all,

   Even decreasing ecutwfc by two orders of magnitude the error
   remains the same. The PBE pseudopotentials are those included in

   https://www.materialscloud.org/discover/sssp/table/
   

   Please help.

    Mensaje reenviado 
   Asunto:  [QE-users] error with qe 6.5
   Fecha:   Fri, 12 Feb 2021 13:49:24 +0100
   De:  José Carlos Conesa Cegarra 
   
   Responder a: Quantum ESPRESSO users Forum
   
   
   Para:Quantum ESPRESSO users Forum
   
   



   Dear all,

   I have found (several times) this error with qe-6.5:


 %%

    Error in routine allocate_fft (1):
    wrong ngm

 %%


    stopping ...

   The input file is attached. Please help

   -- José C. Conesa
   Research Professor
   Instituto de Catálisis y Petroleoquímica, CSIC
   Marie Curie, 2; Campus de Cantoblanco
   28028 Madrid (Spain)
   Phone +34 915854766



   -- El software de antivirus Avast ha analizado este correo  
electrónico en busca de virus.

   https://www.avast.com/antivirus  





Libre de virus. www.avast.com





   <#m_817471404283560405_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
   ___
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   )
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   https://lists.quantum-espresso.org/mailman/listinfo/users
   



--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


___
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--
José C. Conesa
Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie, 2; Campus de Cantoblanco
28028 Madrid (Spain)
Phone +34 915854766




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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Re: [QE-users] Fwd: error with qe 6.5

2021-02-15 Thread Claudio A. Perottoni
Your are using a too small ecutwfc. The table in
https://www.materialscloud.org/discover/sssp/table/ gives you some
suggested wave function cuttoffs (60 Ry for N, for instance). You may also
try the QE input generator
https://www.materialscloud.org/work/tools/qeinputgenerator
Claudio


On Mon, Feb 15, 2021 at 7:33 AM José Carlos Conesa Cegarra <
jccon...@icp.csic.es> wrote:

> I mean,
>
> ecutwfc=1.0D-8
>
> JC Conesa
> El 14/02/2021 a las 20:38, Paolo Giannozzi escribió:
>
> "decreasing" ?
>
> On Sun, Feb 14, 2021 at 8:16 PM José Carlos Conesa Cegarra <
> jccon...@icp.csic.es> wrote:
>
>> Dear all,
>>
>> Even decreasing ecutwfc by two orders of magnitude the error remains the
>> same. The PBE pseudopotentials are those included in
>>
>> https://www.materialscloud.org/discover/sssp/table/
>> Please help.
>>
>>  Mensaje reenviado 
>> Asunto: [QE-users] error with qe 6.5
>> Fecha: Fri, 12 Feb 2021 13:49:24 +0100
>> De: José Carlos Conesa Cegarra 
>> 
>> Responder a: Quantum ESPRESSO users Forum
>>  
>> Para: Quantum ESPRESSO users Forum 
>> 
>>
>> Dear all,
>>
>> I have found (several times) this error with qe-6.5:
>>
>>
>>  
>> %%
>>  Error in routine allocate_fft (1):
>>  wrong ngm
>>
>>  
>> %%
>>
>>  stopping ...
>>
>> The input file is attached. Please help
>>
>> --
>> José C. Conesa
>> Research Professor
>> Instituto de Catálisis y Petroleoquímica, CSIC
>> Marie Curie, 2; Campus de Cantoblanco
>> 28028 Madrid (Spain)
>> Phone +34 915854766
>>
>>
>>
>>
>> --
>> El software de antivirus Avast ha analizado este correo electrónico en busca 
>> de virus.https://www.avast.com/antivirus
>>
>>
>>
>> 
>>  Libre
>> de virus. www.avast.com
>> 
>> <#m_1717585735936729812_m_817471404283560405_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>> ___
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list 
> users@lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>
> --
> José C. Conesa
> Research Professor
> Instituto de Catálisis y Petroleoquímica, CSIC
> Marie Curie, 2; Campus de Cantoblanco
> 28028 Madrid (Spain)
> Phone +34 915854766
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users



-- 

*Claudio A. Perottoni*

Universidade de Caxias do Sul
95070-560 Caxias do Sul - RS - Brazil
http://www.researcherid.com/rid/B-8409-2008
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Re: [QE-users] Fwd: error with qe 6.5

2021-02-15 Thread José Carlos Conesa Cegarra

I mean,

ecutwfc=1.0D-8

JC Conesa

El 14/02/2021 a las 20:38, Paolo Giannozzi escribió:

"decreasing" ?

On Sun, Feb 14, 2021 at 8:16 PM José Carlos Conesa Cegarra 
mailto:jccon...@icp.csic.es>> wrote:


Dear all,

Even decreasing ecutwfc by two orders of magnitude the error
remains the same. The PBE pseudopotentials are those included in

https://www.materialscloud.org/discover/sssp/table/


Please help.

 Mensaje reenviado 
Asunto: [QE-users] error with qe 6.5
Fecha:  Fri, 12 Feb 2021 13:49:24 +0100
De: José Carlos Conesa Cegarra 

Responder a:Quantum ESPRESSO users Forum


Para:   Quantum ESPRESSO users Forum





Dear all,

I have found (several times) this error with qe-6.5:

 
%%
 Error in routine allocate_fft (1):
 wrong ngm
 
%%

 stopping ...

The input file is attached. Please help

-- 
José C. Conesa

Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie, 2; Campus de Cantoblanco
28028 Madrid (Spain)
Phone +34 915854766



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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


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--
José C. Conesa
Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie, 2; Campus de Cantoblanco
28028 Madrid (Spain)
Phone +34 915854766

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Re: [QE-users] Installing Quantum-Espresso on Cluster running Scientific Linux (Red-Hat Derivative)

2021-02-15 Thread Paolo Giannozzi
My limited experience, many years ago, with Scientific Linux was very
negative. Anyway: as long as your software is properly installed, you
should not need anything more complex than "./configure; make [your
targets]" . In my experience the Intel compiler produces the fastest
executables, but gfortran with MKL libraries is also fine.

Paolo

On Mon, Feb 15, 2021 at 5:22 AM Syed Zain Mehmood Bukhari <
glowingsyedzain...@gmail.com> wrote:

> I have set-up a Computer Cluster for computational research work, the
> specifications for the system are attached with this email. The system is
> running on "Scientific Linux release 7.9 (Nitrogen)"
> Kindly guide how to install quantum-espresso on this system ? and which
> compiler will deliver the best compiled version of Quantum Espresso ?
>
> [image: image.png]
>
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] Linear Response and TD-DFPT

2021-02-15 Thread Giuseppe Mattioli


Dear Lucas
TDDFPT is definitely a linear-response method. If you want to read  
something, there is plenty of references in this file


/path-to-your-QE/TDDFPT/README

HTH
Giuseppe

Quoting Lucas Nicolás Lodeiro Moraga :


Hello all,
I am introducing myself into the Time Dependent DFT to compute UV-Vis
spectroscopy. Among the literature, I find that there are two
approximations for that, the Linear Response and the Real Time propagation
approaches...
But, in some codes like CP2K an Quantum ESpresso, the implemented methods
refer to TD-DFPT, which seems to be the linear response approach, but is
not clear to me if this is ok or wrong...
Does somebody know the differences and can give some insight or "simple"
references to clarify me?

Regards - Lucas Lodeiro




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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