[Pw_forum] Bader analysis: CRITIC2

[Ankit Jain]

Dear all,

I have been trying to calculate the bader charges using the approach
suggested at:
http://qe-forge.org/pipermail/pw_forum/2017-May/112779.html

but I am stuck with few questions and is wondering if someone could help me
this.

The steps I am following are as follow:
1. Do pw.x scf run
2. Do pp.x run with plot_num=0 to get electron (pseudo-)charge density and
save in file rho_without_core.cube
3. do critic2 run with:

crystal rho_without_core.cube
load rho_without_core.cube core id rho
zpsp Cl 7 C 4 H 1
rid file rho_with_core.cube field rho

crystal rho_with_core.cube
load rho_with_core.cube id rhoval
integrable rhoval
yt

My questions are:
1. If I am extracting the right charge density from QE using pp.x in step
2? I am extracting electron (pseudo)-charge density
2. If I am specifying right valence electrons in step 3 with zpsp keyword,
especially for Cl, should it be be 7 or 17? Also I need to specify
total_density (rho_with_core.cube in above case) as the argument to
integrable?

Thank You,

Ankit Jain
Stanford University.
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Re: [Pw_forum] Simulation Stops in the middle without any error.

[GAUTAM SHARMA]

There is no wall time for workstation as per my knowledge.


Regards,
Gautam Sharma


On Tue, Jul 25, 2017 at 9:09 PM, Rajesh  wrote:

> Dear Dr Sharma
> Thank you for your response. Actually it's not a cluster, but it's a work
> station. I think wall time is set on clusters. Is there any wall time for
> work station also?
>
> Thank you.
>
> Rajesh
>
> On Jul 25, 2017 21:05, "GAUTAM SHARMA"  iiserpune.ac.in> wrote:
>
>> It can be because your cluster might have some predefined wall time. For
>> instance, a cluster has a wall time of 48 hours ,if your calculations are
>> running longer than 48 hours ​,then you job will stop after 48 hours
>> without giving any error. It can be one possible reason.
>>
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Re: [Pw_forum] Simulation Stops in the middle without any error.

[Rajesh]

Dear Dr Sharma
Thank you for your response. Actually it's not a cluster, but it's a work
station. I think wall time is set on clusters. Is there any wall time for
work station also?

Thank you.

Rajesh

On Jul 25, 2017 21:05, "GAUTAM SHARMA" <
gautam.sha...@students.iiserpune.ac.in> wrote:

> It can be because your cluster might have some predefined wall time. For
> instance, a cluster has a wall time of 48 hours ,if your calculations are
> running longer than 48 hours ​,then you job will stop after 48 hours
> without giving any error. It can be one possible reason.
>
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Re: [Pw_forum] Simulation Stops in the middle without any error.

[GAUTAM SHARMA]

It can be because your cluster might have some predefined wall time. For
instance, a cluster has a wall time of 48 hours ,if your calculations are
running longer than 48 hours ​,then you job will stop after 48 hours
without giving any error. It can be one possible reason.
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[Pw_forum] Heat capacity at constant pressure

[Abolore Musari]

Sir,
I want to know how to calculate the heat capacity at constant pressure
using Quasi harmonic approximation QHA code in quantum espresso package
since the given  examples only show how to calculate the heat capacity at
constant volume.
I would be glad for your kind assistance
Thanks
Musari Abolore
Federal University of Agricuture
Abeokuta,  Nigeria
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Re: [Pw_forum] vc-relax & cell_dofree

[Dr. Thomas Brumme]

Well, it should work and do exactly what it says but it won't respect  
the hexagonal symmetry which might be problematic if you want to  
enforce it. What do you mean with "not appropriate"?
You could also relax the in-plane constant by hand and in this way  
keep the hexagonal symmetry - just make several scf calculations with  
different in-plane constant and fit the total energy with a quadratic  
function to find the minimum...

Another point I noticed - if you want to calculate a 2D MOF maybe the  
metal center doesn't want to stay in the highest symmetry position;  
something like a Jahn-Teller distortion. Maybe the relaxation of the  
cell falls into a wrong minimum because of this. Can you try a  
relaxation without symmetry? Or, maybe just comparing the forces and  
stresses after an scf with symmetry and without to see if this changes  
something...

Thomas


Quoting BARRETEAU Cyrille :

> Thanks for your reply but I am still not very sure I understand well  
> the difference between the two options:
> 'xy' : only v1_x and v2_y are moved
> '2Dxy' : only x and y components are allowed to change
>
> When the vectors v1 and v2 are not orthogonal (which is my case) the  
> option 'xy' is not appropriate ?
>
> Cyrille
>
> 
> Cyrille Barreteau
> CEA Saclay, IRAMIS, SPEC Bat. 771
> 91191 Gif sur Yvette Cedex, FRANCE
> 
> +33 1 69 08 38 56 /+33  6 47 53 66 52  (mobile)
> email: cyrille.barret...@cea.fr
> Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/
> 
> 
> De : pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] de la  
> part de Thomas Brumme [thomas.bru...@uni-leipzig.de]
> Envoyé : mardi 25 juillet 2017 11:32
> À : pw_forum@pwscf.org
> Objet : Re: [Pw_forum] vc-relax & cell_dofree
>
>
> Dear Cyrille,
>
>
> from the input description:
>
> 'xy' : only v1_x and v2_y are moved
>
> '2Dxy' : only x and y components are allowed to change
>
> Thus, even in the case of cell_dofree='xy' I think the cell will  
> change. Anyway, the deviation from 120 DEG is quite small (119.43  
> DEG if I'm not wrong) - I don't know if this could be do to  
> numerical issues. Maybe try starting a new relaxation with a  
> hexagonal cell but smaller in-plane lattice vector of ~99.1%
>
>
> Cheerio
>
>
> Thomas
>
> On 07/25/17 09:08, BARRETEAU Cyrille wrote:
> Dear QE community
>
> I have a question related to vc-relax and the option cell_dofree.
> I want to relax a 2D metal-organic framework (MOF) with hexagonal  
> lattice (ibrav=4)
> Could you please explain what is the difference between  
> cell-dofree=xy and cell_dofree=2Dxy?
>
> I have noticed that when using cell_dofree=2Dxy the final  
> CELL_PARAMETER is no longer perfectly hexagonal (see below). Should  
> I use cell_dofree=xy instead and why?
>
> final:
> CELL_PARAMETERS (alat= 25.44640422)
>0.990921488  -0.000187347   0.0
>   -0.495622997   0.858299558   0.0
>0.0   0.0   0.742630080
>
> Thanks in advance
>
> Cyrille
>
> 
> Cyrille Barreteau
> CEA Saclay, IRAMIS, SPEC Bat. 771
> 91191 Gif sur Yvette Cedex, FRANCE
> 
> +33 1 69 08 38 56 /+33  6 47 53 66 52  (mobile)
> email: cyrille.barret...@cea.fr
> Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/
> 
> 
>
>
>
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> --
> Dr. rer. nat. Thomas Brumme
> Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
> Leipzig University
> Phillipp-Rosenthal-Strasse 31
> 04103 Leipzig
>
> Tel:  +49 (0)341 97 36456
>
> email: thomas.bru...@uni-leipzig.de



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Re: [Pw_forum] vc-relax & cell_dofree

[BARRETEAU Cyrille]

Thanks for your reply but I am still not very sure I understand well the 
difference between the two options:
'xy' : only v1_x and v2_y are moved
'2Dxy' : only x and y components are allowed to change

When the vectors v1 and v2 are not orthogonal (which is my case) the option 
'xy' is not appropriate ?

Cyrille


Cyrille Barreteau
CEA Saclay, IRAMIS, SPEC Bat. 771
91191 Gif sur Yvette Cedex, FRANCE

+33 1 69 08 38 56 /+33  6 47 53 66 52  (mobile)
email: cyrille.barret...@cea.fr
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/


De : pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] de la part de 
Thomas Brumme [thomas.bru...@uni-leipzig.de]
Envoyé : mardi 25 juillet 2017 11:32
À : pw_forum@pwscf.org
Objet : Re: [Pw_forum] vc-relax & cell_dofree


Dear Cyrille,


from the input description:

'xy' : only v1_x and v2_y are moved

'2Dxy' : only x and y components are allowed to change

Thus, even in the case of cell_dofree='xy' I think the cell will change. 
Anyway, the deviation from 120 DEG is quite small (119.43 DEG if I'm not wrong) 
- I don't know if this could be do to numerical issues. Maybe try starting a 
new relaxation with a hexagonal cell but smaller in-plane lattice vector of 
~99.1%


Cheerio


Thomas

On 07/25/17 09:08, BARRETEAU Cyrille wrote:
Dear QE community

I have a question related to vc-relax and the option cell_dofree.
I want to relax a 2D metal-organic framework (MOF) with hexagonal lattice 
(ibrav=4)
Could you please explain what is the difference between cell-dofree=xy and 
cell_dofree=2Dxy?

I have noticed that when using cell_dofree=2Dxy the final CELL_PARAMETER is no 
longer perfectly hexagonal (see below). Should I use cell_dofree=xy instead and 
why?

final:
CELL_PARAMETERS (alat= 25.44640422)
   0.990921488  -0.000187347   0.0
  -0.495622997   0.858299558   0.0
   0.0   0.0   0.742630080

Thanks in advance

Cyrille


Cyrille Barreteau
CEA Saclay, IRAMIS, SPEC Bat. 771
91191 Gif sur Yvette Cedex, FRANCE

+33 1 69 08 38 56 /+33  6 47 53 66 52  (mobile)
email: cyrille.barret...@cea.fr
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/





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Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig

Tel:  +49 (0)341 97 36456

email: thomas.bru...@uni-leipzig.de

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Re: [Pw_forum] vc-relax & cell_dofree

[Thomas Brumme]

Dear Cyrille,


from the input description:

'xy' : only v1_x and v2_y are moved

'2Dxy' : only x and y components are allowed to change

Thus, even in the case of cell_dofree='xy' I think the cell will change. 
Anyway, the deviation from 120 DEG is quite small (119.43 DEG if I'm not 
wrong) - I don't know if this could be do to numerical issues. Maybe try 
starting a new relaxation with a hexagonal cell but smaller in-plane 
lattice vector of ~99.1%



Cheerio


Thomas


On 07/25/17 09:08, BARRETEAU Cyrille wrote:

Dear QE community

I have a question related to vc-relax and the option cell_dofree.
I want to relax a 2D metal-organic framework (MOF) with hexagonal 
lattice (ibrav=4)
Could you please explain what is the difference between cell-dofree=xy 
and cell_dofree=2Dxy?


I have noticed that when using cell_dofree=2Dxy the final 
CELL_PARAMETER is no longer perfectly hexagonal (see below). Should I 
use cell_dofree=xy instead and why?


final:
CELL_PARAMETERS (alat= 25.44640422)
   0.990921488  -0.000187347   0.0
  -0.495622997   0.858299558   0.0
   0.0   0.0   0.742630080

Thanks in advance

Cyrille


*Cyrille Barreteau*
CEA Saclay, IRAMIS, SPECBat. 771
91191 Gif sur Yvette Cedex, FRANCE

+33 1 69 08 38 56 /+33 6 47 53 66 52 (mobile)
email: cyrille.barret...@cea.fr
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/




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Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig

Tel:  +49 (0)341 97 36456

email: thomas.bru...@uni-leipzig.de

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Re: [Pw_forum] Supercell for fcc lattice (ibrav=2)

[Thomas Brumme]

Dear Uttam Paliwal,

Another approach would be to use simple geometry and to create the cell 
by hand. This also helps to understand structures instead of using some 
program - which I can only recommend to do once you need to create more 
complex structures or have more complicated materials.


Regards

Thomas


On 07/25/17 09:24, Jess Wellendorff wrote:


This would be a very easy task if you used Virtual NanoLab for 
manipulating atomistic structures and setting up your QE input files:


http://docs.quantumwise.com/tutorials/espresso.html

Regards,

Jess Wellendorff, PhD


On 07/25/2017 09:18 AM, Uttam Paliwal wrote:

Hi
How to construct and imply a 2x2x2 supercell for ibrav=2 i.e. cubic 
fcc lattice of rock-salt NaCl type structure having space group 225.
also suggest how to get atomic position for it. My single unit cell 
input file is as


&CONTROL
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  outdir = '/OUT PUT DIR' ,
  pseudo_dir = '/TEMP' ,
  prefix = 'p' ,

 /
 &SYSTEM
   ibrav = 2,
   celldm(1) = 9.07124,
 nat = 2,
ntyp = 2,
 ecutwfc = 60.0 ,
 ecutrho = 500.0 ,
 space_group = 225 ,
 /
 &ELECTRONS
conv_thr = 1.0d-8 ,
 mixing_mode = 'plain' ,

 /
ATOMIC_SPECIES
   Cd  112.41100  Cd.pbe-dn-rrkjus_psl.0.3.1.UPF
O   16.0  O_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS crystal_sg
   Cd  0.00.00.0
O  0.50.50.5
K_POINTS automatic
  12 12 12   0 0 0




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QuantumWise A/S
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Email:jess.wellendo...@quantumwise.com
Tel:   +45 69901888
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Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig

Tel:  +49 (0)341 97 36456

email: thomas.bru...@uni-leipzig.de

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Re: [Pw_forum] Supercell for fcc lattice (ibrav=2)

[Jess Wellendorff]

This would be a very easy task if you used Virtual NanoLab for 
manipulating atomistic structures and setting up your QE input files:


http://docs.quantumwise.com/tutorials/espresso.html

Regards,

Jess Wellendorff, PhD


On 07/25/2017 09:18 AM, Uttam Paliwal wrote:

Hi
How to construct and imply a 2x2x2 supercell for ibrav=2 i.e. cubic 
fcc lattice of rock-salt NaCl type structure having space group 225.
also suggest how to get atomic position for it. My single unit cell 
input file is as


&CONTROL
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  outdir = '/OUT PUT DIR' ,
  pseudo_dir = '/TEMP' ,
  prefix = 'p' ,

 /
 &SYSTEM
   ibrav = 2,
   celldm(1) = 9.07124,
 nat = 2,
ntyp = 2,
 ecutwfc = 60.0 ,
 ecutrho = 500.0 ,
 space_group = 225 ,
 /
 &ELECTRONS
conv_thr = 1.0d-8 ,
 mixing_mode = 'plain' ,

 /
ATOMIC_SPECIES
   Cd  112.41100  Cd.pbe-dn-rrkjus_psl.0.3.1.UPF
O   16.0  O_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS crystal_sg
   Cd  0.00.00.0
O  0.50.50.5
K_POINTS automatic
  12 12 12   0 0 0




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QuantumWise A/S
Fruebjergvej 3, Postbox 4
2100 Copenhagen, Denmark
Web:   www.quantumwise.com
Email: jess.wellendo...@quantumwise.com
Tel:   +45 69901888
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[Pw_forum] Supercell for fcc lattice (ibrav=2)

[Uttam Paliwal]

Hi
How to construct and imply a 2x2x2 supercell for ibrav=2 i.e. cubic fcc
lattice of rock-salt NaCl type structure having space group 225.
also suggest how to get atomic position for it. My single unit cell input
file is as

&CONTROL
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  outdir = '/OUT PUT DIR' ,
  pseudo_dir = '/TEMP' ,
  prefix = 'p' ,

 /
 &SYSTEM
   ibrav = 2,
   celldm(1) = 9.07124,
 nat = 2,
ntyp = 2,
 ecutwfc = 60.0 ,
 ecutrho = 500.0 ,
 space_group = 225 ,
 /
 &ELECTRONS
conv_thr = 1.0d-8 ,
 mixing_mode = 'plain' ,

 /
ATOMIC_SPECIES
   Cd  112.41100  Cd.pbe-dn-rrkjus_psl.0.3.1.UPF
O   16.0  O_pbe_v1.2.uspp.F.UPF
ATOMIC_POSITIONS crystal_sg
   Cd  0.00.00.0
O  0.50.50.5
K_POINTS automatic
  12 12 12   0 0 0
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[Pw_forum] vc-relax & cell_dofree

[BARRETEAU Cyrille]

Dear QE community

I have a question related to vc-relax and the option cell_dofree.
I want to relax a 2D metal-organic framework (MOF) with hexagonal lattice 
(ibrav=4)
Could you please explain what is the difference between cell-dofree=xy and 
cell_dofree=2Dxy?

I have noticed that when using cell_dofree=2Dxy the final CELL_PARAMETER is no 
longer perfectly hexagonal (see below). Should I use cell_dofree=xy instead and 
why?

final:
CELL_PARAMETERS (alat= 25.44640422)
   0.990921488  -0.000187347   0.0
  -0.495622997   0.858299558   0.0
   0.0   0.0   0.742630080

Thanks in advance

Cyrille


Cyrille Barreteau
CEA Saclay, IRAMIS, SPEC Bat. 771
91191 Gif sur Yvette Cedex, FRANCE

+33 1 69 08 38 56 /+33  6 47 53 66 52  (mobile)
email: cyrille.barret...@cea.fr
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/


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