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

[Juniper Savchick]

To all,

It is my understanding that in material science the crystal lattice
structure is an FCC structure with 4 extra atoms inside of it. My PhD
supervisor describes it as two overlapping FCC lattice structures. To
create a visualization of this structure you must define the positions of
18 atoms where most of those atoms are only partially inside the unit cell.
Therefore we say that there are 8 Carbon atoms inside the diamond crystal
lattice structure. However, when you perform MD calculations you must use
whole atoms because fractional atoms are non-physical. Therefore I need to
define the position of 18 atoms to model the entire diamond crystal lattice.

I was under the impression that the ibrav parameter in cp.x was used to
fill out the remaining atomic positions based on the two atomic positions
we define in the input file. I would like to verify this by defining my own
atomic positions and using the CELL_PARAMETERS section of the cp.x input
(ibrav=0). However, when I do this cp.x gives infinite or null data output
values for energy and pressure.

I am confused as to why my "18atom.txt" input (see google drive link in
original message) will not work properly. I have a decent understanding of
the physics but am confused about implementation via cp.x. I have been
using Avogadro2 to visualize each structure, generate atomic positions and
lattice vectors, and then implement this data into my cp.x input files.
This method works fine when I define 8 atoms but once I try to scale up to
all 18 atoms cp.x gives the aforementioned nonsensical outputs.

Does anyone have any recommendations for how I can get my "18atom.txt"
input file to execute properly?

Sincerely,
Juniper Savchick
Graduate Assistant
Virginia Commonwealth University

 QE inputs
<https://drive.google.com/drive/folders/1BLY8nVULkYzAWleKz-n6nwjFaKHc_U4m>


On Mon, Feb 28, 2022 at 2:31 PM Juniper Savchick <curly363 at gmail.com> wrote:

> 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
>
>  QE inputs
> <https://drive.google.com/drive/folders/1BLY8nVULkYzAWleKz-n6nwjFaKHc_U4m>
>
>
>
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