[QE-users] Phonon Density of States by atomic type

Wed Aug 5 08:47:10 CEST 2020

> 1) The columns are not labeled.  Do they follow the order that the atoms 
> are defined in my scf input file or is there some other ordering method?

yes

> 
> 2) Can these partial densities of state be calculated when the phonon 
> run is done with q in band form rather than with a grid of q 
> points(ldisp=true)?  

I think it should be possible, but it does not make any sense. The DOS 
is an integral over the k-points in the BZ : if you integrate over 
something else, you can get whatever you want.

> My attempt resulted in a crash fairly quickly.  I 
> have been trying to move to calculating only specific paths rather than 
> entire dispersions because moving from single unit cells to supercells 
> has been a real introduction to the scaling issues of phonon calculations.

It should not be particularly slow. Maybe if you have a system with a 
lot of atoms...

> 
> Thanks,
> Brad
> 
> --------------------------------------------------------
> Bradly Baer
> Graduate Research Assistant, Walker Lab
> Interdisciplinary Materials Science
> Vanderbilt University
> 
> 
> ------------------------------------------------------------------------
> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of 
> Pietro Davide Delugas <pdelugas at sissa.it>
> *Sent:* Tuesday, August 4, 2020 1:54 AM
> *To:* users at lists.quantum-espresso.org <users at lists.quantum-espresso.org>
> *Subject:* Re: [QE-users] Phonon Density of States by atomic type
> That's weird
> I just checked the 6.5, the printout of atomic projected dos is there
> have a look at matdyn.f90
> at line 762 you should have
> 
> IF (ionode) WRITE (2, '(2ES18.10,1000ES12.4)') E, SUM(DOSofE(1:nat)), 
> DOSofE(1:nat)
> 
> 
> 
> On 8/4/20 12:12 AM, Baer, Bradly wrote:
>> Actually, I just found this message in the mailing list archive.  I 
>> must have missed it due to poor word choice while searching originally.
>>
>> https://lists.quantum-espresso.org/pipermail/users/2018-March/040476.html 
>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fpipermail%2Fusers%2F2018-March%2F040476.html&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C61b3cf5c6c1243b767d508d838434800%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637321208925373249&sdata=V0lriJQbM%2BBL4%2F7ZNJQIDj58wGhgiWriUj4ItRjjv7Q%3D&reserved=0>
>>
>> It appears that this functionality was added in 2018, but I am unsure 
>> on how to check if this was something that was ever merged into the 
>> main distribution of QE(I am using 6.5) or if it is limited to the 
>> development branch or even only available through manual patching.  Is 
>> there some way for me to check or should I just attempt to apply the 
>> patch and see what happens?
>>
>> -Brad
>>
>> --------------------------------------------------------
>> Bradly Baer
>> Graduate Research Assistant, Walker Lab
>> Interdisciplinary Materials Science
>> Vanderbilt University
>>
>>
>> ------------------------------------------------------------------------
>> *From:* users <users-bounces at lists.quantum-espresso.org> 
>> <mailto:users-bounces at lists.quantum-espresso.org> on behalf of Baer, 
>> Bradly <bradly.b.baer at Vanderbilt.Edu> 
>> <mailto:bradly.b.baer at Vanderbilt.Edu>
>> *Sent:* Monday, August 3, 2020 4:49 PM
>> *To:* Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org> 
>> <mailto:users at lists.quantum-espresso.org>
>> *Subject:* Re: [QE-users] Phonon Density of States by atomic type
>> Professor Marzari, I had generally followed the process of pw.x -> 
>> ph.x -> q2r.x ->Matdyn.x(dos)/matdyn.x(dispersion) -> plot.  I am 
>> assuming that is what you mean by interpolating to build the DOS 
>> myself?  Would you have any recommendations on resources/references to 
>> extend that process into obtaining the contributions from each atomic 
>> type?
>>
>>
>> To Pietro: I just went back and looked through some output files and I 
>> was unable to find the information you were referring to.  My .dos 
>> file only has two columns.  Below is both the input and output from 
>> the dos matdyn.x calculation. Perhaps I am doing something wrong?
>>
>> _INPUT - GaNMatdyn.in_
>>  &input
>>     asr='simple',
>>     flfrc='GaN444.fc', dos=.true.
>>     fldos='phonon.dos', nk1=50, nk2=50, nk3=50
>>  /
>>
>> _OUTPUT_
>>  -1.6359E+02  0.0000E+00
>>  -1.6259E+02  5.7394E-05
>> .
>> .
>> .
>> .
>>   6.9341E+02  1.6180E-05
>>   6.9441E+02  0.0000E+00
>>
>>
>>
>> -Brad
>> --------------------------------------------------------
>> Bradly Baer
>> Graduate Research Assistant, Walker Lab
>> Interdisciplinary Materials Science
>> Vanderbilt University
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Nicola Marzari <nicola.marzari at epfl.ch> 
>> <mailto:nicola.marzari at epfl.ch>
>> *Sent:* Monday, August 3, 2020 1:03 PM
>> *To:* Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org> 
>> <mailto:users at lists.quantum-espresso.org>; Baer, Bradly 
>> <bradly.b.baer at Vanderbilt.Edu> <mailto:bradly.b.baer at Vanderbilt.Edu>
>> *Subject:* Re: [QE-users] Phonon Density of States by atomic type
>> On 03/08/2020 18:39, Baer, Bradly wrote:
>> > Hello,
>> > 
>> > I was consulting the reference materials on materialsproject.org 
>> > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaterialsproject.org%2Fmaterials%2Fmp-830%2F&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=bv9GSN8yKAoo5CMizuZAgkP0yaGPSRyKxzr0bgKtawI%3D&reserved=0 
>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaterialsproject.org%2Fmaterials%2Fmp-830%2F&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C61b3cf5c6c1243b767d508d838434800%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637321208925373249&sdata=6GYLnK4uImXg8p3SA3FD9qsWcvhucTLL5jqXHkUFOY0%3D&reserved=0>> for 
>> a semiconductor.
>> > In the section on phonon results, they had the phonon density of states 
>> > plotted with the contributions of each type of atom as well as the total 
>> > DOS.    I have calculated the DOS of a system before using QE, but only 
>> > did the total DOS of the system.  Does QE have the capability to give 
>> > similar results?
>> > 
>> > Thanks,
>> > Brad
>>
>>
>> Dear Brad,
>>
>>
>> for phonons I do not think there is any ready-made tool (but I could be
>> wrong). For phonon dispersions, we have implemented an online phonon
>> visulizer, based on the code by Henrique Miranda:
>> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fwork%2Ftools%2Finteractivephonon&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=1T2HLQ694J5aEvZ%2FLgQP50VfjNfQ6qhsGa5QOZwfIL8%3D&reserved=0 
>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fwork%2Ftools%2Finteractivephonon&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C61b3cf5c6c1243b767d508d838434800%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637321208925383252&sdata=pSdGp69pwB2Bb%2F4BC5qFkynLq2%2BZlSC2lTXfrXhwUhk%3D&reserved=0>
>> that allows you to explore graphically/interactively phonon dispersions
>> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fdiscover%2F2dstructures%2Fdetails%2FBN&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=Bgt18WK%2BonmwRVsgdpE3ciA6RnG6W7F9z8KoDxyEBAM%3D&reserved=0 
>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fdiscover%2F2dstructures%2Fdetails%2FBN&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C61b3cf5c6c1243b767d508d838434800%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637321208925383252&sdata=krYKTN9SFW74QNwQECUtdBkctsvR9EGHjCPykl8mo6c%3D&reserved=0>
>>
>> For the phonon DOS, if you have done a calculation with QE, you can at
>> zero cost interpolate/diagonalize the dynamical matrices on fine q
>> meshes, and build the DOS yourself. But maybe others have some tool
>> ready to use.
>>
>>                         nicola
>>
>>
>> > 
>> > --------------------------------------------------------
>> > Bradly Baer
>> > Graduate Research Assistant, Walker Lab
>> > Interdisciplinary Materials Science
>> > Vanderbilt University
>> > 
>> > 
>> > 
>> > _______________________________________________
>> > Quantum ESPRESSO is supported by MaX (https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2Fquantum-espresso&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=Jt03%2Bj5ro6IG5HmpkwSHFewqTqwjbvevDrJ12BFWXQk%3D&reserved=0 
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>> > 
>>
>>
>> -- 
>> ----------------------------------------------------------------------
>> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
>> Director, National Centre for Competence in Research NCCR MARVEL, EPFL
>> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftheossrv1.epfl.ch%2FMain%2FContact&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344711366&sdata=69b6UN%2Bwxc8IsOtHrgcqaQNdClTXzhGhly1KVsplAHU%3D&reserved=0 
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>>
>> _______________________________________________
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> 
> 
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