[QE-users] Phonon Density of States by atomic type
Baer, Bradly
bradly.b.baer at Vanderbilt.Edu
Tue Aug 4 22:20:54 CEST 2020
I am embarrassed to say that I was indeed looking at an archived calculation that was in the wrong spot. It was run on ver 6.2 and thus was missing the new bits. I repeated the calculation in 6.5 and the additional columns showed as you guys indicated. Sorry about my confusion!
Two additional questions, if I may continue to impose:
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?
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)? 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.
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
>
>
>
> _______________________________________________
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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
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