[QE-users] Raman intensities in quantum espresso (Paolo Giannozzi)
Banhi Chatterjee
Banhi.Chatterjee at ijs.si
Wed Jun 16 12:13:41 CEST 2021
Dear Paolo,
Thank you very much for the reply. I shall try it uncommenting the line
lraman=.true.
Regards
Banhi
On 2021-06-16 12:00, users-request at lists.quantum-espresso.org wrote:
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> 1. Re: How to make bulk to 0D system (Lorenzo Paulatto)
> 2. Re: How to make bulk to 0D system (Matthew Marcus)
> 3. Re: MD runs out of memory with increasing number of cores
> (Paolo Giannozzi)
> 4. Re: Raman intensities in quantum espresso (Paolo Giannozzi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 15 Jun 2021 20:55:27 +0200
> From: Lorenzo Paulatto <paulatz at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Cc: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] How to make bulk to 0D system
> Message-ID: <A17FD036-7CF1-49D7-B05D-D1749580AC99 at getmailspring.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Shivam,
> you can use some graphical tool, probably, or do it by hand. I
> personally do not use any external tool, I cannot advice you there.
> With some simple computing software like matlab/octave, or python or
> even excel, it does not take that long, and it becomes easier every
> time.
>
> Once you have put all the atoms in the right place, be sure to put
> them in a large enough cell to have 10-20? of vacuum around to avoid
> images from interacting.
> kind regards
> --
> Lorenzo Paulatto - Paris
> On Jun 15 2021, at 9:49 am, Shivam Kansara <sidkans23 at gmail.com> wrote:
>> Dear all,
>> I am Shivam Kansara and wish to work on nanoparticle systems. I wish
>> to make a bulk system into nanoparticles (0D). So how to make
>> nanoparticles from bulk systems e.g. FeO or CoO. ?
>> Please help me in this regard.
>>
>> Thanking you in advance
>>
>> --
>>
>>
>> -- With Regards
>> Dr. Shivam Kansara
>>
>>
>> Web: https://scholar.google.co.in/citations?user=gucGzjsAAAAJ&hl=en
>> https://www.researchgate.net/profile/Shivam_Kansara
>>
>>
>> https://sites.google.com/view/shivamkansara
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>> 06/15/21, 12:35:48 PM
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>> _______________________________________________
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> Message: 2
> Date: Tue, 15 Jun 2021 18:51:04 -0700
> From: Matthew Marcus <mamarcus at lbl.gov>
> To: users at lists.quantum-espresso.org
> Subject: Re: [QE-users] How to make bulk to 0D system
> Message-ID: <de5dfa7c-eda5-95bb-8d37-a5e14070247c at lbl.gov>
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>
> CrystalMaker is a really cool tool which can do that kind of thing.
> It's graphical and reads cif files. You can use it
> to make a superlattice then edit out the atoms you don't want.
> There's also the command-line cif2cell tool which I know
> can make slabs, so it can surely carve out nanos bounded by given
> crystal planes. I assume the bulk is the rocksalt
> structure, in which case you'd want to bound by 111-family planes to
> get an octahedron or tetrahedron or 100 for a cube.
> For a cuboctahedron or something similar, you'd need to make a
> combination of cuts.
>
> Sincerely,
> Matthew Marcus
>
> On 6/15/2021 11:55 AM, Lorenzo Paulatto wrote:
>> Hello Shivam,
>> you can use some graphical tool, probably, or do it by hand. I
>> personally do not use any external tool, I cannot advice you there.
>> With? some simple computing software like matlab/octave, or python or
>> even excel, it does not take that long, and it becomes easier every
>> time.
>>
>> Once you have put all the atoms in the right place, be sure to put
>> them in a large enough cell to have 10-20? of vacuum around to avoid
>> images from interacting.
>>
>> kind regards
>>
>> --
>> Lorenzo Paulatto - Paris
>> On Jun 15 2021, at 9:49 am, Shivam Kansara <sidkans23 at gmail.com>
>> wrote:
>>
>> Dear all,
>> I am Shivam Kansara and wish to work on nanoparticle systems. I
>> wish to make a bulk system into nanoparticles (0D). So how?to
>> make?nanoparticles from bulk systems e.g. FeO or CoO. ?
>> Please help me in this regard.
>>
>> Thanking?you in advance
>>
>> --
>>
>> *-- With Regards*
>> Dr. Shivam Kansara
>> Web:https://scholar.google.co.in/citations?user=gucGzjsAAAAJ&hl=en
>> <https://scholar.google.co.in/citations?user=gucGzjsAAAAJ&hl=en>
>> https://www.researchgate.net/profile/Shivam_Kansara
>> <https://www.researchgate.net/profile/Shivam_Kansara>
>> https://sites.google.com/view/shivamkansara
>> <https://sites.google.com/view/shivamkansara>
>>
>> Mailtrack
>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
>> Sender notified by
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>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&>
>> 06/15/21, 12:35:48 PM
>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.org
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> ------------------------------
>
> Message: 3
> Date: Wed, 16 Jun 2021 07:32:40 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] MD runs out of memory with increasing number
> of cores
> Message-ID:
> <CAPMgbCsd9Uo7WJMe1ZRs7r2Kpb1E5rszWtSkaX6dzZQEJhCjkg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hard to say without knowing exactly what goes out of which memory
> limits.
> Note that not all arrays are distributed across processors, so a
> considerable number of arrays are replicated on all processes. As a
> consequence the total amount of required memory will increase with the
> number of mpi processes. Also note that a 128-atom cell is not "large"
> and
> 144 cores are not "a small number of processors". You will not get any
> advantage by just increasing the number of processors any more, quite
> the
> opposite. If you have too many idle cores, you should consider
> - "task group" parallelization (option -ntg)
> - MPI+OpenMP parallelization (configure --enable-openmp)
> Please also note that ecutwfc=80 Ry is a rather large cutoff for a USPP
> (while ecutrho=320 is fine) and that running with K_POINTS Gamma
> instead of
> 1 1 1 0 0 0 will be faster and take less memory.
>
> Paolo
>
> On Mon, Jun 14, 2021 at 4:22 PM Lenz Fiedler <fiedler.lenz at gmail.com>
> wrote:
>
>> Dear users,
>>
>> I am trying to perform a MD simulation for a large cell (128 Fe atoms,
>> gamma point) using pw.x and I get a strange scaling behavior. To test
>> the
>> performance I ran the same MD simulation with an increasing number of
>> nodes
>> (2, 4, 6, 8, etc.) using 24 cores per node. The simulation is
>> successful
>> when using 2, 4, and 6 nodes, so 48, 96 and 144 cores resp (albeit
>> slow,
>> which is within my expectations for such a small number of
>> processors).
>> Going to 8 and more nodes, I run into an out-of-memory error after
>> about
>> two time steps.
>> I am a little bit confused as to what could be the reason. Since a
>> smaller
>> amount of cores works I would not expect a higher number of cores to
>> run
>> without an oom error as well.
>> The 8 node run explictly outputs at the beginning:
>> " Estimated max dynamical RAM per process > 140.54 MB
>> Estimated total dynamical RAM > 26.35 GB
>> "
>>
>> which is well within the 2.5 GB I have allocated for each core.
>> I am obviously doing something wrong, could anyone point to what it
>> is?
>> The input files for a 6 and 8 node run can be found here:
>> https://drive.google.com/drive/folders/1kro3ooa2OngvddB8RL-6Iyvdc07xADNJ?usp=sharing
>> I am using QE6.6.
>>
>> Kind regards
>> Lenz
>>
>> PhD Student (HZDR / CASUS)
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.org
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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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> Message: 4
> Date: Wed, 16 Jun 2021 07:51:17 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Raman intensities in quantum espresso
> Message-ID:
> <CAPMgbCurWNqWDhxwTtszDSfKfkPdHtEZosWT1gfbM9+Vg9d1aQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> If Raman coefficients are correctly computed, there will be a column
> labelled "Raman" and one "depol.fact" (depolarization factor) in the
> output
> of dynmat.x. You can plot it the way you prefer. Note that the
> calculation
> of Raman cross sections was disabled in example15.
>
> Paolo
>
> On Fri, Jun 4, 2021 at 9:17 PM Banhi Chatterjee
> <Banhi.Chatterjee at ijs.si>
> wrote:
>
>> Dear users,
>>
>> I have calculated the normal modes around Gamma point of a compound
>> using
>> ph.x.
>>
>> All my modes are Raman active. I have followed example15 in the
>> tutorials
>> of the
>>
>> release q-e-qe-6.7MaX-Release.tar.gz.
>>
>> After completing the phonon calculations I run dynmat.x.
>>
>> Then I extract and plot the Raman frequecies and intensities
>>
>> using the following two commands.
>>
>> awk ?NR==1,/mode/{next}/DYNMAT/,NR==0{next}{print}? si.dm.out >
>> plotdata_si.dat
>>
>> plot ?plotdata_si.dat? u ($2):($3) title ? si-RAMAN? w i lw 2
>>
>> I want to clarify if this is the correct way to extract the Raman
>> intensities. If not,
>>
>> where can I find how to do this in an appropriate way.
>>
>> Thanking you,
>>
>> Banhi Chatterjee
>> --
>> Dr. Banhi Chatterjee
>> Post-doctoral researcher
>> Jozef stefan Institute, Ljubljana, Slovenia
>> e-mail: Banhi.Chatterjee at ijs.si
>> banhiphy at gmail.com
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at 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
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--
Dr. Banhi Chatterjee
Post-doctoral researcher
Jozef stefan Institute, Ljubljana, Slovenia
e-mail: Banhi.Chatterjee at ijs.si
banhiphy at gmail.com
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