Re: [QE-users] Crystallographic group determination

2019-03-31 Thread Ankit Sharma 
Hi,
Thank you very much for the reply Dr. Conesa.
As a follow up question, is it a convention to represent the symmetry of
the primitive unit cell as that of the conventional cell because by looking
at the crystal structure of the primitive unit cell for the above mentioned
system i.e Gallium Oxide, it appears to be triclinic and hence the P1
symmetry.

Thank You,
Ankit Sharma
University at Buffalo


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On Sun, Mar 31, 2019 at 12:55 PM Ankit Sharma  wrote:

> Hi,
> I am working with Gallium Oxide which has a 20 atom conventional cell with
> the space group of *C2/m *and a 10 atom primitive cell with space group
> of *P1 *(materials project):
> https://materialsproject.org/materials/mp-886/#.
>
> When I run scf calculations on conventional cell the output clearly states
> as *C2/m *symmetry, but for the primitive cell too, the output is again
> *C2/m*.
> I am unable to figure out the reason for it. Am I missing something? Any
> help in this regard will be greatly appreciated. Attached is the cif file
> from the materials project for reference for both the conventional and the
> primitive unit cells and the input and output files for the fake run to
> determine the symmetry.
>
> Thank You,
> Ankit Sharma
> University at Buffalo
>
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Re: [QE-users] Comparison of output from ev.x executable with pressure versus distance obtained from direct numerical derivation

2019-03-31 Thread Nicolas Leconte 
Hi Lorenzo and Paolo,

Thanks for your responses.

Numerical derivation in the sense of deriving the energy with distance to
get the force, and derive by the surface to get the pressure.

For both fit and derivation, between 3.0 and 3.6 Angstrom, I used 1000
points (through interpolation of the DFT data). I further tested it with
1500 points (where I had to change the hard-coded limit for the size of one
of the vectors in ev.f90). It did not change the behavior much.

I would also imagine it to be accidental, but I was surprised to see such a
good agreement. So I was vaguely hoping for some misunderstanding from my
part or even a bug in the code I was not aware of.

Option 2, among the 4 options, Birch-Murnaghan was giving best agreement,
which seems to make sense due to the higher order terms. But maybe by
reducing the range of compression I could get a better agreement. Right
now, compression from 3.4 to 3.0 Ang of my bilayer interlayer distance
requires about 10 GPa.

Maybe that's too much to hope for a good equation of state fitting?

Regards,
Nicolas

On Mon, Apr 1, 2019 at 4:19 AM Paolo Giannozzi 
wrote:

> On Sun, Mar 31, 2019 at 4:34 PM Lorenzo Paulatto 
> wrote:
>
> My guess is that the chisq (chi squared?)
>>
>
> yes, chi squared, as usually defined: (1/N) \sum_{i=1}^N (E_i^{fit}-E_i)^2
>
> factor is purely accidental.
>>
>
> I cannot but agree
>
> Paolo
>
>>
>> Regards
>>
>> --
>> Lorenzo Paulatto CNRS /SU
>> Written on a virtual keyboard with real fingers
>>
>> On Sun, 31 Mar 2019, 05:23 Nicolas Leconte, 
>> wrote:
>>
>>> Dear QE users,
>>>
>>> I have recently used the ev.x executable to obtain the equation of state
>>> from my energy versus volume data.
>>>
>>> When I compare the Birch Murnaghan (B-M) 3d order equation of state
>>> results with a direct numerical derivation, I obtain the best matching
>>> between both methods. Yet, there is still some mismatch.
>>>
>>> I tried reducing my data to only include smaller pressures and reduce
>>> the impact of higher order terms, but it doesn't really change much, while
>>> I thought it would.
>>>
>>> Then, while playing with my output data, I noticed that simply
>>> multiplying my pressure curve from B-M with the value of chisq, I get
>>> perfect agreement between both methods.
>>>
>>> Am I missing something as on how to use the output from this script. It
>>> feels like too good a coincidence.
>>>
>>> Now, I wonder what precludes me from using this chisq as a prefactor to
>>> the bulk modulus B0 (
>>> https://en.wikipedia.org/wiki/Birch%E2%80%93Murnaghan_equation_of_state)
>>> to obtain a proper agreement with the numerically derived curve.
>>>
>>> Regards,
>>> Nicolas
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>>> users@lists.quantum-espresso.org
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>>
>> ___
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>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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Re: [QE-users] Comparison of output from ev.x executable with pressure versus distance obtained from direct numerical derivation

2019-03-31 Thread Paolo Giannozzi 
On Sun, Mar 31, 2019 at 4:34 PM Lorenzo Paulatto  wrote:

My guess is that the chisq (chi squared?)
>

yes, chi squared, as usually defined: (1/N) \sum_{i=1}^N (E_i^{fit}-E_i)^2

factor is purely accidental.
>

I cannot but agree

Paolo

>
> Regards
>
> --
> Lorenzo Paulatto CNRS /SU
> Written on a virtual keyboard with real fingers
>
> On Sun, 31 Mar 2019, 05:23 Nicolas Leconte, 
> wrote:
>
>> Dear QE users,
>>
>> I have recently used the ev.x executable to obtain the equation of state
>> from my energy versus volume data.
>>
>> When I compare the Birch Murnaghan (B-M) 3d order equation of state
>> results with a direct numerical derivation, I obtain the best matching
>> between both methods. Yet, there is still some mismatch.
>>
>> I tried reducing my data to only include smaller pressures and reduce the
>> impact of higher order terms, but it doesn't really change much, while I
>> thought it would.
>>
>> Then, while playing with my output data, I noticed that simply
>> multiplying my pressure curve from B-M with the value of chisq, I get
>> perfect agreement between both methods.
>>
>> Am I missing something as on how to use the output from this script. It
>> feels like too good a coincidence.
>>
>> Now, I wonder what precludes me from using this chisq as a prefactor to
>> the bulk modulus B0 (
>> https://en.wikipedia.org/wiki/Birch%E2%80%93Murnaghan_equation_of_state)
>> to obtain a proper agreement with the numerically derived curve.
>>
>> Regards,
>> Nicolas
>> ___
>> users mailing list
>> users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> ___
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> users@lists.quantum-espresso.org
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] Crystallographic group determination

2019-03-31 Thread José C . Conesa 

Hi,

The primitive cell has always the same symmetry as the conventional one. 
You may specify all the atoms in the primitive cell, and give all cell 
dimensions and angles, as if the cell were of P1 symmetry; but the 
program will cleverly find out the correct space group.


JC Conesa

El 31/03/2019 a las 18:55, Ankit Sharma escribió:

Hi,
I am working with Gallium Oxide which has a 20 atom conventional cell 
with the space group of *C2/m *and a 10 atom primitive cell with space 
group of *P1 *(materials project): 
https://materialsproject.org/materials/mp-886/#.


When I run scf calculations on conventional cell the output clearly 
states as *C2/m *symmetry, but for the primitive cell too, the output 
is again *C2/m*.
I am unable to figure out the reason for it. Am I missing something? 
Any help in this regard will be greatly appreciated. Attached is the 
cif file from the materials project for reference for both the 
conventional and the primitive unit cells and the input and output 
files for the fake run to determine the symmetry.


Thank You,
Ankit Sharma
University at Buffalo

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--
José C. Conesa
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie 2, Cantoblanco
28049 Madrid, Spain
Tel. (+34)915854766



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[QE-users] Crystallographic group determination

2019-03-31 Thread Ankit Sharma 
Hi,
I am working with Gallium Oxide which has a 20 atom conventional cell with
the space group of *C2/m *and a 10 atom primitive cell with space group of *P1
*(materials project): https://materialsproject.org/materials/mp-886/#.

When I run scf calculations on conventional cell the output clearly states
as *C2/m *symmetry, but for the primitive cell too, the output is again
*C2/m*.
I am unable to figure out the reason for it. Am I missing something? Any
help in this regard will be greatly appreciated. Attached is the cif file
from the materials project for reference for both the conventional and the
primitive unit cells and the input and output files for the fake run to
determine the symmetry.

Thank You,
Ankit Sharma
University at Buffalo


Ga2O3_conventional.cif
Description: Binary data


Ga2O3_mp-886_primitive.cif
Description: Binary data


Ga2O3.scf.in
Description: Binary data


Ga2O3.scf.out
Description: Binary data


Ga2O3conv.scf.in
Description: Binary data


Ga2O3conv.scf.out
Description: Binary data
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Re: [QE-users] Comparison of output from ev.x executable with pressure versus distance obtained from direct numerical derivation

2019-03-31 Thread Lorenzo Paulatto 
Dear Nicolas,
What do you mean by direct numerical derivation? How many points did you
use for the fit, and for the derivation? My guess is that the chisq (chi
squared?) factor is purely accidental.

Regards

-- 
Lorenzo Paulatto CNRS /SU
Written on a virtual keyboard with real fingers

On Sun, 31 Mar 2019, 05:23 Nicolas Leconte, 
wrote:

> Dear QE users,
>
> I have recently used the ev.x executable to obtain the equation of state
> from my energy versus volume data.
>
> When I compare the Birch Murnaghan (B-M) 3d order equation of state
> results with a direct numerical derivation, I obtain the best matching
> between both methods. Yet, there is still some mismatch.
>
> I tried reducing my data to only include smaller pressures and reduce the
> impact of higher order terms, but it doesn't really change much, while I
> thought it would.
>
> Then, while playing with my output data, I noticed that simply multiplying
> my pressure curve from B-M with the value of chisq, I get perfect agreement
> between both methods.
>
> Am I missing something as on how to use the output from this script. It
> feels like too good a coincidence.
>
> Now, I wonder what precludes me from using this chisq as a prefactor to
> the bulk modulus B0 (
> https://en.wikipedia.org/wiki/Birch%E2%80%93Murnaghan_equation_of_state)
> to obtain a proper agreement with the numerically derived curve.
>
> Regards,
> Nicolas
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> users@lists.quantum-espresso.org
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