[QE-users] Defining C diamond structure cp.x

Mon Feb 28 21:27:16 CET 2022

Professor Michal Husak,

Thank you for taking the time to help me with this. I would greatly
appreciate an example input file for the QE executable cp.x. However, I am
slightly confused as to how you incorporate the space group number into the
cp.x input file as there is no parameter for this in the input file
description for cp.x. I only see "space_group" in the pw.x input file
description (which I appreciate you pointing out for me) but I need to
define a carbon diamond crystal within the cp.x input file specifically.
Could you clarify your method for me please? (This can wait until you are
prepared to send the example input tomorrow as I am sure you are very busy).

A GUI for converting from CIF to various QE inputs would be invaluable to
me and I would greatly appreciate access to such a resource.

Thank you for your time and help with this matter. I look forward to
hearing from you.

Sincerely,
Juniper Savchick
Graduate Assistant
Virginia Commonwealth University

On Mon, Feb 28, 2022 at 3:08 PM Stefano Baroni <baroni at sissa.it> wrote:

> Thank you, Michal. When you are done, please share your converter with the
> community. You may eve want to consider distributing it with QE. Thanks and
> best wishes to all. SB
>
> ___
> Stefano Baroni, Trieste -- http://stefano.baroni.me
>
> > On 28 Feb 2022, at 20:45, Husak Michal <Michal.Husak at vscht.cz> wrote:
> >
> > The most save and correct way is not to use ibraw, but space group
> number ...
> > I will generate correct diamond for you toomorow (I work
> > with my students on CIF->QE convertor with GUI ...
> > But diamond is so simple, it can be done by hand ....
> > You need just the SG number (i do not remember Fd3m number)
> > and only 1 atom in 0,0,0 ...
> >
> > Michal Husak
> > UCT Prague
> > ________________________________
> > From: users <users-bounces at lists.quantum-espresso.org> on behalf of
> Juniper Savchick <curly363 at gmail.com>
> > Sent: Monday, February 28, 2022 8:31:49 PM
> > To: users at lists.quantum-espresso.org
> > Subject: [QE-users] Defining C diamond structure cp.x
> >
> > Hello,
> >
> > I am a graduate assistant at Virginia Commonwealth University and I am
> using Quantum Espresso to perform CP molecular dynamics calculations. I
> would like to run a simple set up of a single Carbon Diamond crystal
> structure. My ultimate research goal is to generate equations of state for
> warm dense matter, starting with Carbon in a diamond structure. It is my
> understanding that there are multiple ways to input this system into
> Quantum Espresso but I am not getting the same results with each method. I
> want to make sure I have an intimate understanding of the cp.x executable.
> This is why I want to calculate the same system using different inputs. (I
> am using QE 7.0) I have tried many different input methods with the main
> differences being the number of atoms that are explicitly defined. (2,8,&
> 18)
> >
> > It is my understanding that if you use input parameter ibrav=2 where 2
> atoms are explicitly defined under "ATOMIC_POSITIONS", this is the carbon
> diamond primitive cell. Based on QE related literature, cp.x will
> automatically fill in the remaining atoms to complete the carbon diamond
> crystal structure. I am skeptical that cp.x is actually doing this. Most of
> the QE related literature pertained to pw.x so perhaps each executable
> defines the crystal structure differently? I have looked into documentation
> for both cp.x and pw.x to no avail. I would appreciate anyone who can help
> clarify this input for me.
> >
> > If you use input parameter ibrav=0 then you should be able to explicitly
> define all 18 atoms that comprise the conventional carbon diamond lattice
> structure. However, if I try to use ibrav=0 and explicitly define 18 atomic
> positions I get infinite values as outputs. My next attempt was to use
> ibrav=0 and explicitly define 8 atomic positions. The 8 atom run gave
> reasonable values but the pressure was orders of magnitude smaller than the
> 2 atom run. This is concerning to me and it has become clear that I am
> misunderstanding the cp.x input. I have scoured QE forums and documentation
> to no avail.
> >
> > At this point it would seem the most accurate method is the 8 atom run
> since I can use these positions to generate a supercell that has the
> periodic carbon diamond structure, albeit with vacancies in some of the
> corners and sides. I assume if I make the supercell large enough the errors
> due to imperfections will be negligible. Also, no real structure is
> perfectly periodic so we should still be able to use the 8 atom unit cell
> to construct at usable supercell for modeling purposes. Does this
> assumption sound reasonable?
> >
> > To summarize by questions:
> > What is the most accurate way to input the carbon diamond crystal
> structure in cp.x?
> > Why does ibrav=0 with 18 atoms explicitly defined not work?
> > Is my understanding of how to input the primitive cell in cp.x correct?
> > Is my assumption regarding the "8 atom generated supercell" reasonable?
> >
> > I understand this is quite a bit to ask but I am at a loss for what to
> do next. I would appreciate any help that can be offered. I have provided
> example input files for each type of input described. (see google drive
> link)
> >
> > Sincerely,
> > Juniper Savchick
> > Graduate Assistant
> > Virginia Commonwealth University
> > BS Physics, minor Mathematics
> > Pursuing a PhD in Mechanical and Nuclear Engineering
> >
> > [
> https://drive-thirdparty.googleusercontent.com/16/type/application/vnd.google-apps.folder+shared]
> QE inputs<
> https://drive.google.com/drive/folders/1BLY8nVULkYzAWleKz-n6nwjFaKHc_U4m>
> >
> >
> > _______________________________________________
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