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Today's Topics:
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 <[email protected]>
To: Quantum ESPRESSO users Forum <[email protected]>
Cc: Quantum ESPRESSO users Forum <[email protected]>
Subject: Re: [QE-users] How to make bulk to 0D system
Message-ID: <[email protected]>
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 <[email protected]> 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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Message: 2
Date: Tue, 15 Jun 2021 18:51:04 -0700
From: Matthew Marcus <[email protected]>
To: [email protected]
Subject: Re: [QE-users] How to make bulk to 0D system
Message-ID: <[email protected]>
Content-Type: text/plain; charset=windows-1252; format=flowed
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 <[email protected]>
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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06/15/21, 12:35:48 PM
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------------------------------
Message: 3
Date: Wed, 16 Jun 2021 07:32:40 +0200
From: Paolo Giannozzi <[email protected]>
To: Quantum ESPRESSO users Forum <[email protected]>
Subject: Re: [QE-users] MD runs out of memory with increasing number
of cores
Message-ID:
<capmgbcsd9uo7wjme1zrs7r2kpb1e5rszwtskax6dzzqejhc...@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 <[email protected]>
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)
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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 <[email protected]>
To: Quantum ESPRESSO users Forum <[email protected]>
Subject: Re: [QE-users] Raman intensities in quantum espresso
Message-ID:
<capmgbcurwnqwdhxwttszdsfkfkpdhtezoswt1gfbm9+vg9d...@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
<[email protected]>
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: [email protected]
[email protected]
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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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