[Pw_forum] charge density of KS state in SOC calculation

[Wei Li]

Dear QE users and developers,

I want to plot the charge density with SOC effects, but as known that the
SOC effects via:

lspinorb=.true.,
noncolin = .true.,

would lead to (two) degenerated KS orbitals compared with every KS orbital
in NON-SOC case, so which orbital should be plotted into order to look into
how SOC affect the charge density distribution compared with NON-SOC case?

thanks in advance

Wei

--
State Key Lab of Theoretical &
 Computational Chemistry
 Institute of Theoretical Chemistry
 Jilin University
 Changchun, 130023
 P.R. China
 Email: liwei0...@gmail.com
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Re: [Pw_forum] charge density

[Uri Argaman]

Dear Alexandra Davila

I also publish a message about this subject a few days ago. I also think it
something with the pseudopotential but I check it also for norm-conserving
pseudopotential and I have the same problem. In your message you write:

"From each file I obtain different values 6.79 and 7.42 respectively." What
are exactly these values? These values are the same of all the values of
the charge differences which should be zero? Do you use plot_num=9?

I note that I am not a developer but I am using QE for a long time.



Uri Argaman

Ben-Gurion University

Israel
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[Pw_forum] charge density

[Alexandra Davila]

   Dear QE users,
 I am interested on charge density difference. But first I made a test
 and calculate the number of electrons of an atom (for example #e=7).
 In order to do that I use the pp.x and obtain two files xxx.charge and
 pp.out(XCrysDens format). From each file I obtain different values 6.79
 and 7.42 respectively. If I increase the system (#electrons= 1440), the
 difference is bigger: 1397.38 and 1476.9. Why?
 I have calculated the same with other program (but also with other
 pseudopotential) and I obtain the right number. The reason could be due
 to the pseudopotential, for my QE calculations I am using GRBV
 pseudopotentials.
 Thanks,

-- 
A. Dávila
AG. Pehlke
Institut für Theoretische Physik und Astrophysik
Christian-Albrechts-Universität zu Kiel
Leibnizstr. 15
24118 Kiel

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Re: [Pw_forum] charge density vizualization using xcrysden

[Joshua Davis]

VESTA can read the xcrysden grid file, as well

Joshua Davis
Michigan State University - Chemistry Dept.

On Sun, Aug 21, 2016 at 2:14 PM Joshua Davis 
wrote:

> VESTA can read the xcrysden grid file, as well
>
> On Sun, Aug 21, 2016 at 12:36 PM Arles V. Gil Rebaza 
> wrote:
>
>> Hi, if you have a .cube file, you can use VMD, to have very nice picture.!
>>
>> Best
>>
>> A.V. Gil Rebaza
>> IFLP - Argentina
>>
>> 2016-08-21 12:47 GMT-03:00 Manu Hegde :
>>
>>> Hello,
>>> Xcrysden does a good job, I think there is some example (look in PP
>>> folder) on how to code charge density using gnuplot.
>>>
>>> On Sun, Aug 21, 2016 at 11:38 AM, Uri Argaman 
>>> wrote:
>>>
 Dear QE users and devalopers
 I visualize charge density in three dimensions but I do not succeed to
 show only a part of the unit cell using xcrysden (I do the calculation for
 large unit cell). I can do that using xcrysden or I need other
 visualization tool? In case it cannot be done using xcrysden, which
 visualization tool is recommended for 3d charge density?
 Thank you very much
 Uri Argaman
 Ben-Gurion University
 Israel


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>>>
>>>
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>>
>>
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Re: [Pw_forum] charge density vizualization using xcrysden

[Joshua Davis]

VESTA can read the xcrysden grid file, as well

On Sun, Aug 21, 2016 at 12:36 PM Arles V. Gil Rebaza 
wrote:

> Hi, if you have a .cube file, you can use VMD, to have very nice picture.!
>
> Best
>
> A.V. Gil Rebaza
> IFLP - Argentina
>
> 2016-08-21 12:47 GMT-03:00 Manu Hegde :
>
>> Hello,
>> Xcrysden does a good job, I think there is some example (look in PP
>> folder) on how to code charge density using gnuplot.
>>
>> On Sun, Aug 21, 2016 at 11:38 AM, Uri Argaman 
>> wrote:
>>
>>> Dear QE users and devalopers
>>> I visualize charge density in three dimensions but I do not succeed to
>>> show only a part of the unit cell using xcrysden (I do the calculation for
>>> large unit cell). I can do that using xcrysden or I need other
>>> visualization tool? In case it cannot be done using xcrysden, which
>>> visualization tool is recommended for 3d charge density?
>>> Thank you very much
>>> Uri Argaman
>>> Ben-Gurion University
>>> Israel
>>>
>>>
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>
>
>
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Re: [Pw_forum] charge density vizualization using xcrysden

[Arles V. Gil Rebaza]

Hi, if you have a .cube file, you can use VMD, to have very nice picture.!

Best

A.V. Gil Rebaza
IFLP - Argentina

2016-08-21 12:47 GMT-03:00 Manu Hegde :

> Hello,
> Xcrysden does a good job, I think there is some example (look in PP
> folder) on how to code charge density using gnuplot.
>
> On Sun, Aug 21, 2016 at 11:38 AM, Uri Argaman 
> wrote:
>
>> Dear QE users and devalopers
>> I visualize charge density in three dimensions but I do not succeed to
>> show only a part of the unit cell using xcrysden (I do the calculation for
>> large unit cell). I can do that using xcrysden or I need other
>> visualization tool? In case it cannot be done using xcrysden, which
>> visualization tool is recommended for 3d charge density?
>> Thank you very much
>> Uri Argaman
>> Ben-Gurion University
>> Israel
>>
>>
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>
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Re: [Pw_forum] charge density vizualization using xcrysden

[Manu Hegde]

Hello,
Xcrysden does a good job, I think there is some example (look in PP folder)
on how to code charge density using gnuplot.

On Sun, Aug 21, 2016 at 11:38 AM, Uri Argaman 
wrote:

> Dear QE users and devalopers
> I visualize charge density in three dimensions but I do not succeed to
> show only a part of the unit cell using xcrysden (I do the calculation for
> large unit cell). I can do that using xcrysden or I need other
> visualization tool? In case it cannot be done using xcrysden, which
> visualization tool is recommended for 3d charge density?
> Thank you very much
> Uri Argaman
> Ben-Gurion University
> Israel
>
>
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[Pw_forum] charge density vizualization using xcrysden

[Uri Argaman]

Dear QE users and devalopers
I visualize charge density in three dimensions but I do not succeed to show
only a part of the unit cell using xcrysden (I do the calculation for large
unit cell). I can do that using xcrysden or I need other visualization
tool? In case it cannot be done using xcrysden, which visualization tool is
recommended for 3d charge density?
Thank you very much
Uri Argaman
Ben-Gurion University
Israel
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Re: [Pw_forum] charge density espresso 5.0.1

[Mostafa Youssef]

Dear  Sakhraoui,


The format of .XSF is explained here:

http://www.xcrysden.org/doc/XSF.html


You can plot rho_up -rho_down using plot_num=6 option in pp.x

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html#idm6483344



Regards,
Mostafa
MIT
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[Pw_forum] charge density espresso 5.0.1

[taoufik espresso]

Dear all,

by using espresso-5.0.1, i calculated the charge density of the FeRh/MgO
junction. My question is how the generated xsf file is organized?

I want to plot the difference rho (up) – rho (down).
any suggestion will be appreciated
cheers


=
Sakhraoui Taoufik, Phd student
Laboratoire de la Matière Condensée & Nanosciences
Faculté des sciences de Monastir
Avenue de l'environnement 5019-Monastir,Tunisie
tel. :(+216) 96 173 454 || 22 618 579
email : tsakhr...@yahoo.com
=
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[Pw_forum] charge density plot - really too small!

[Mohamad Moadeli]

Dear all,

I am trying to create a 2D charge plot, but the following error appears...

===
[mohammad@localhost Downloads]$ ~/espresso-5.2.0/bin/plotrho.x
Input file > charge2D
r0   :   0.  0.  0.
tau1 :   0.  1.  0.
tau2 :   0.  0.  6.
read  35 atomic positions
output file > charge2D.ps
Read 100 *100  grid
Bounds:-0.023.439000
min, max, # of levels > -0.023.439000 19
 really too small!
[mohammad@localhost Downloads]$
===

Please suggest me, how to solve the problem?

Regards,

Mohammad Moaddeli,

Chahid Chamran University of Ahvaz
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Re: [Pw_forum] Charge density minus atomic ones

[Paolo Giannozzi]

Yes, the code computes the superposition of atomic charges, as found in the
pseudopotential files, and subtracts it from the valence charge. Note that
- the superposition of atomic charges is done in reciprocal space: Fourier
components exceeding the cutoff will be "lost"
- the atomic charges in pseudopotential files are typically computed for
the atomic reference configuration used in the generation of the
pseudopotential, not always coinciding with the ground state

Paolo

On Sat, Apr 2, 2016 at 9:20 PM, Juan Jose Melendez Martinez <
melen...@unex.es> wrote:

> Dear all
>
> We want to calculate the change in the electronic density when a molecule
> is added to a crystal frame. We have seen that pp.x allows one (plot_num 9)
> calculate the actual electronic density minus the superposition of the
> atomic ones. Our question is: how does QE calculate the reference
> electronic density, that is, the superposition of atomic ones? My guess it
> that it builds it from the pseudopotential file, so that only one run is
> enough. Is this right?
>
> Thanks in advance.
>
> Juanjo
>
> Dr. Juan J. Meléndez Martínez
> Dpt. of Physics
> University of Extremadura
> Avda. de Elvas, s/n 06006 Badajoz (Spain)
>
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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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[Pw_forum] Charge density minus atomic ones

[Juan Jose Melendez Martinez]

Dear all

We want to calculate the change in the electronic density when a molecule is 
added to a crystal frame. We have seen that pp.x allows one (plot_num 9) 
calculate the actual electronic density minus the superposition of the atomic 
ones. Our question is: how does QE calculate the reference electronic density, 
that is, the superposition of atomic ones? My guess it that it builds it from 
the pseudopotential file, so that only one run is enough. Is this right?

Thanks in advance.

Juanjo

Dr. Juan J. Meléndez Martínez
Dpt. of Physics
University of Extremadura
Avda. de Elvas, s/n 06006 Badajoz (Spain)

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Re: [Pw_forum] Charge Density Difference Calculation problem

[Lorenzo Paulatto]

On Thursday, December 17, 2015 09:32:04 AM luca maggi wrote:
> Serial version
>  Reading header from file  slub_no_hubb.charge
> At line 119 of file plot_io.f90 (unit = 4, file = 'slub_no_hubb.charge')
> Fortran runtime error: Bad integer for item 1 in list input


Well, how did you generate this file?

kind regards

-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/
23-24/4é16 Boîte courrier 115, 
4 place Jussieu 75252 Paris Cédex 05

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[Pw_forum] Charge Density Difference Calculation problem

[luca maggi]

Dear All,
I'm trying to calculate the charge density   difference between the same 
structure with and without the hubbard correction term. I have calculated 
already the charge density for the two structure.
The input file for getting the difference  is :

&inputpp
/
 &plot
  iflag = 3 ,
  nfile = 2   ,
  filepp(1) = 'slub_no_hubb.charge' ,weight(1) = -1.0
  filepp(2) = 'slub_hubb.charge' , weight(2) =  1.0
  output_format =3,
  nx = 100 ,
  ny = 100 ,
  nz = 100 ,
  fileout= 'cdd.dat' ,
/
 and the error is :

Serial version
 Reading header from file  slub_no_hubb.charge
At line 119 of file plot_io.f90 (unit = 4, file = 'slub_no_hubb.charge')
Fortran runtime error: Bad integer for item 1 in list input

Anynone may help me ?

Best regards

Luca Maggi

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Re: [Pw_forum] charge density

[Paolo Giannozzi]

If I remember correctly the charge density of the self-consistent
calculation is not overwritten by a non-scf calculation.

Paol

On Mon, Oct 26, 2015 at 2:40 AM, Jiqiang Li  wrote:

> Dear all,
>   can anybody tell me whether the charge density from scf calculation
> would be overrided in a nscf calculation?
>   Thanks in advance!
>
> Jiqiang Li
>
> --
>
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-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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[Pw_forum] charge density

[Jiqiang Li]

Dear all,
  can anybody tell me whether the charge density from scf calculation would 
be overrided in a nscf calculation?
  Thanks in advance!

Jiqiang Li



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[Pw_forum] charge density

[Raj kamal]

I calculated the charge density difference plot using VESTA for
understanding the bonding mechanism between adsorbent and adsorbate. The
system I used here is Li adsorbed on carbon based substrate and it was
shown in the figure.  Yellow and Blue colors are represents the positive
and negative value of isosurface. And i am struggling to interpret my
results in terms of electron accumulation and depletion region with these
two colour loops and the isosurface value also. *What is the exact physical
meaning of this + and – isosurface value and these two colours represents
what?accumlation and depletion*. And are there any rules to choose the
isosurface value. But I feel using the 2D slice model may explain more
detail about the bonding mechanism between adsorbent and adsorbate but am
beginner of this tool so can anyone please explain how to prooced for 2D
display slice model for the same system.

   [image: Inline image 2]
-- 
*Best regards,*
*Rajkamal.A.*
*Research Scholar,(SRM UNIV).*
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Re: [Pw_forum] charge density unit

[Mohamad Moadeli]

Thank you so much

regards,

Mohammad

On Thu, Jul 16, 2015 at 12:50 AM, Paolo Giannozzi 
wrote:

> Sure it is: things like this do not change all the time! Paolo
>
> On Wed, Jul 15, 2015 at 10:14 PM, Mohamad Moadeli <
> mohammad.moadd...@gmail.com> wrote:
>
>> Dear all,
>>
>> I searched the forum for charge density unit and I found:
>>
>> ===
>>
>> Dong-Hee Lim wrote:
>>
>> >* I was just wondering what unit of charge density is used in Quantum
>> *>* Espresso and Xcrysden viewer.
>> *
>> the viewer just visualizes. Quantum-Espresso uses atomic units
>> (Rydberg for PWscf, Hartree for CP, unfortunately). The charge
>> density is not multiplied by "e" if I remember correctly, so it
>> has the dimensions of 1/V, i.e. 1/(bohr radii)^3
>>
>> Paolo
>> --
>> Paolo Giannozzi, Democritos and University of Udine, Italy
>>
>> ===
>>
>> Is it still valid in espresso-5.1.1 ?
>>
>> Best regards,
>>
>> Mohammad Moaddeli
>>
>> Shahid Chamran University of Ahvaz
>>
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>
>
>
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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Re: [Pw_forum] charge density unit

[Paolo Giannozzi]

Sure it is: things like this do not change all the time! Paolo

On Wed, Jul 15, 2015 at 10:14 PM, Mohamad Moadeli <
mohammad.moadd...@gmail.com> wrote:

> Dear all,
>
> I searched the forum for charge density unit and I found:
>
> ===
>
> Dong-Hee Lim wrote:
>
> >* I was just wondering what unit of charge density is used in Quantum
> *>* Espresso and Xcrysden viewer.
> *
> the viewer just visualizes. Quantum-Espresso uses atomic units
> (Rydberg for PWscf, Hartree for CP, unfortunately). The charge
> density is not multiplied by "e" if I remember correctly, so it
> has the dimensions of 1/V, i.e. 1/(bohr radii)^3
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
> ===
>
> Is it still valid in espresso-5.1.1 ?
>
> Best regards,
>
> Mohammad Moaddeli
>
> Shahid Chamran University of Ahvaz
>
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-- 
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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[Pw_forum] charge density unit

[Mohamad Moadeli]

Dear all,

I searched the forum for charge density unit and I found:

===

Dong-Hee Lim wrote:

>* I was just wondering what unit of charge density is used in Quantum
*>* Espresso and Xcrysden viewer.
*
the viewer just visualizes. Quantum-Espresso uses atomic units
(Rydberg for PWscf, Hartree for CP, unfortunately). The charge
density is not multiplied by "e" if I remember correctly, so it
has the dimensions of 1/V, i.e. 1/(bohr radii)^3

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

===

Is it still valid in espresso-5.1.1 ?

Best regards,

Mohammad Moaddeli

Shahid Chamran University of Ahvaz
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Re: [Pw_forum] Charge Density

[Mohamad Moadeli]

Thank you so much for clear explanations.

Best,

Mohammad

On Mon, Jul 6, 2015 at 12:49 PM, Giovanni Cantele <
giovanni.cant...@spin.cnr.it> wrote:

> the iflag variable, as far as I remember, is needed only to convert what
> is computed as specified in the INPUTPP name list in a format that cam be
> visualised using different graphic tools (such as gunplay, XCrysDen, and so
> on).
>
> If you what to use average.x you only need the file containing the charge
> density or the potential (as computed using INPUTPP), and then use
> average.x.
>
> Giovanni
>
>
> On 04 Jul 2015, at 00:29, Mohamad Moadeli 
> wrote:
>
> Dear all,
>
> To show interface dipoles, I am trying to calculate charge density for a
> 2D combined system containing Ag adsorbed on graphene sheet, like what is
> done in a sample attached (rho_tot). The vacuum space is provided along
> the z axis. Is it right to do the following steps?
>
> 1- Running a SCF
>
> 2- Performing a PP calculation:
> &inputpp
>   plot_num=0,
> &plot
>   nfile=1
>   filepp(1)='sys.charge'
>   iflag=2,
>   output_format=3,
>   e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
>   e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
>   x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
>   nx=40, ny=40
>   fileout='sys.charge001.dat'
>  /
>
> 
>
> What if I set  iflag=3,  and finally run average.x ?
>
> Any help will be greatly appreciated.
>
> Best,
>
> Mohammad,
>
> Shahid Chamran University of Ahvaz
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>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cant...@spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
>
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Re: [Pw_forum] Charge Density

[Giovanni Cantele]

the iflag variable, as far as I remember, is needed only to convert what is 
computed as specified in the INPUTPP name list in a format that cam be 
visualised using different graphic tools (such as gunplay, XCrysDen, and so on).

If you what to use average.x you only need the file containing the charge 
density or the potential (as computed using INPUTPP), and then use average.x.

Giovanni


> On 04 Jul 2015, at 00:29, Mohamad Moadeli  wrote:
> 
> Dear all,
> 
> To show interface dipoles, I am trying to calculate charge density for a 2D 
> combined system containing Ag adsorbed on graphene sheet, like what is done 
> in a sample attached (rho_tot). The vacuum space is provided along the z 
> axis. Is it right to do the following steps?
> 
> 1- Running a SCF
> 
> 2- Performing a PP calculation:
> &inputpp
>   plot_num=0,
> &plot
>   nfile=1
>   filepp(1)='sys.charge'
>   iflag=2,
>   output_format=3,
>   e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
>   e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
>   x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
>   nx=40, ny=40
>   fileout='sys.charge001.dat'
>  /
> 
> 
> 
> What if I set  iflag=3,  and finally run average.x ?
> 
> Any help will be greatly appreciated.
> 
> Best,
> 
> Mohammad,
> 
> Shahid Chamran University of Ahvaz
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele

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[Pw_forum] Charge Density

[Mohamad Moadeli]

Dear all,

To show interface dipoles, I am trying to calculate charge density for a 2D
combined system containing Ag adsorbed on graphene sheet, like what is done
in a sample attached (rho_tot). The vacuum space is provided along the z
axis. Is it right to do the following steps?

1- Running a SCF

2- Performing a PP calculation:
&inputpp
  plot_num=0,
&plot
  nfile=1
  filepp(1)='sys.charge'
  iflag=2,
  output_format=3,
  e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
  e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
  x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
  nx=40, ny=40
  fileout='sys.charge001.dat'
 /



What if I set  iflag=3,  and finally run average.x ?

Any help will be greatly appreciated.

Best,

Mohammad,

Shahid Chamran University of Ahvaz
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Re: [Pw_forum] charge density difference plots between two strained structures (Paolo Giannozzi)

[Rajdeep Banerjee]

Dear Prof. P. Giannozzi,
   thanks a lot for the suggestion.
I'll surely look into it.

Thanks and regards,
Rajdeep Banerjee
PhD student
JNCASR, Bangalore,
India
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Re: [Pw_forum] charge density difference plots between two strained structures

[Paolo Giannozzi]

If the strain is small and if FFT dimensions are the same, you may try
to force the code to ignore the different structures of the two cases
and just plot the difference between the unstrained charge and the
strained one on the same grid. Not sure what you will obtain, through!

Paolo

On Sat, 2014-12-06 at 18:08 +0530, Rajdeep Banerjee wrote:
> Dear all,
>  how to generate charge density difference plots (3D) for
> a system between two strain values(alat is different, because alat =
> (1+e)*a0 where e and a0 are strain and equilibrium lattice constants
> respectively), because the generated 3D grids will different for the
> above cases.
> 
> 
> Thanks and regards,
> Rajdeep Banerjee
> PhD student
> JNCASR, Bangalore,
> India
> ___
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[Pw_forum] charge density difference plots between two strained structures

[Rajdeep Banerjee]

Dear all,
 how to generate charge density difference plots (3D) for a
system between two strain values(alat is different, because alat = (1+e)*a0
where e and a0 are strain and equilibrium lattice constants respectively),
because the generated 3D grids will different for the above cases.

Thanks and regards,
Rajdeep Banerjee
PhD student
JNCASR, Bangalore,
India
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[Pw_forum] Charge density Grid

[Paolo Giannozzi]

On Tue, 2014-08-05 at 11:33 -0400, Kayahan Saritas wrote:

> pp.x document says that I can use output_format = 3 to manipulate grid
> density, otherwise grid density is taken from FFT grid (or Fourier
> components are used), however it doesn?t seem to work even though I
> tried all possible 3D options for output_format.  

when everything else fails, read the ... code:

  ! are vectors defining the plotting region aligned along xyz ?
  !
  fast3d = ( e1(2) == 0.d0  .and.  e1(3) == 0.d0) .and. &
   ( e2(1) == 0.d0  .and.  e2(3) == 0.d0) .and. &
   ( e3(1) == 0.d0  .and.  e3(2) == 0.d0)
  !
  ! are crystal axis aligned along xyz ?
  !
  fast3d = fast3d .and. &
   ( at(2,1) == 0.d0  .and.  at(3,1) == 0.d0) .and. &
   ( at(1,2) == 0.d0  .and.  at(3,2) == 0.d0) .and. &
   ( at(1,3) == 0.d0  .and.  at(2,3) == 0.d0)

  fast3d = fast3d .and. (trim(interpolation) == 'fourier')
  !
  !Initialise FFT for rho(r) => rho(G) conversion if needed
  !
  IF (.not. ( iflag == 3 .and. ( output_format == 5 .or. &
 output_format == 6 .or. &
 fast3d ) ) ) THEN
the case you want is active if the above is true. If you have 
set iflag == 3 and output_format == 3 or 4 and it still doesn't 
work, this means that "fast3d" is true, which happens if both the
desired axis and the crystal axis lie along the three cartesian 
axis. Since the code tries hard not to use Fourier interpolation
in 3D (it is awfully slow), in this case the entire grid is chosen.
This is however not consistent with what the documentation says,
though. You may either modify the code the hard way, or try
"interpolation='bspline'"

P.

> 
> 
> Input file:
> 
> 
> &INPUTPP
> outdir='./'
> prefix='in'
> plot_num=0
> spin_component=0
> filplot='tmp_dens'
> /
> &PLOT
> nfile=1
> output_format=3
> fileout='density.xsf'
> iflag=3
> e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
> e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
> e3(1)=0.0, e3(2)=0.0, e3(3)=1.0,
> x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
> nx=144, ny=144, nz=144
> /
> 
> 
> Thanks,
> 
> 
> Saritas Kayahan
> PhD Student
> Grossman Group
> Office: 13-4069
> Cell: +1-617-955-3981
> Office: +1-617-258-8741
> Email: kayahan at mit.edu
> 
> 
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] Charge density Grid

[Kayahan Saritas]

Thank you Paolo. I modified the input file as you requested, but still output 
doesn?t change. It still looks 216x216x216.

pp.x document says that I can use output_format = 3 to manipulate grid density, 
otherwise grid density is taken from FFT grid (or Fourier components are used), 
however it doesn?t seem to work even though I tried all possible 3D options for 
output_format.  

Input file:

&INPUTPP
outdir='./'
prefix='in'
plot_num=0
spin_component=0
filplot='tmp_dens'
/
&PLOT
nfile=1
output_format=3
fileout='density.xsf'
iflag=3
e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
e3(1)=0.0, e3(2)=0.0, e3(3)=1.0,
x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
nx=144, ny=144, nz=144
/

Thanks,

Saritas Kayahan
PhD Student
Grossman Group
Office: 13-4069
Cell: +1-617-955-3981
Office: +1-617-258-8741
Email: kayahan at mit.edu



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[Pw_forum] Charge density Grid

[Paolo Giannozzi]

You need to specify three axis e0, e1, e2 and an origin x0,
if I remember correctly

P.

On Mon, 2014-08-04 at 19:54 -0400, Kayahan Saritas wrote:
> Dear PWSCF users,
> 
> 
> Do you know how to set grid density in pp.x input file? I guess I have
> to set output format as 3, so that I can play with grid density
> otherwise it is automatically taken from FFT grid. However at the end,
> still my output charge density grid is 216x216x216. Below you can find
> my input file. 
> 
> 
> &INPUTPP
> outdir='./'
> prefix='in'
> plot_num=0
> spin_component=0
> filplot='density.dens'
> /
> 
> 
> &PLOT
> nfile=1
> output_format=3
> fileout=?density.cube'
> iflag=3
> 
> 
> nx=144
> ny=144
> nz=144
> /
> 
> 
> Thanks,
> 
> 
> Saritas Kayahan
> PhD Student
> Grossman Group
> Office: 13-4069
> Email: kayahan at mit.edu
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] Charge density Grid

[Kayahan Saritas]

Dear PWSCF users,

Do you know how to set grid density in pp.x input file? I guess I have to set 
output format as 3, so that I can play with grid density otherwise it is 
automatically taken from FFT grid. However at the end, still my output charge 
density grid is 216x216x216. Below you can find my input file. 

&INPUTPP
outdir='./'
prefix='in'
plot_num=0
spin_component=0
filplot='density.dens'
/

&PLOT
nfile=1
output_format=3
fileout=?density.cube'
iflag=3

nx=144
ny=144
nz=144
/

Thanks,

Saritas Kayahan
PhD Student
Grossman Group
Office: 13-4069
Email: kayahan at mit.edu






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[Pw_forum] Charge density with and without the electric field

[Mudit Dixit]

Dear Hadi Arefi,
Thank you so much for your kind help. I found your reply very helpful.





On 21 February 2014 20:03, Hadi Arefi  wrote:

>  Dear Mudit,
>
>
>
> I couldn't find a 'charge density difference plot' in supplementary
> information but I assume they just calculated the charge density for those
> two structures that you mentioned, and subtracted from each other. The
> result can be plotted as a distribution of charge in 3D (2D) or you can add
> up the values to get a number for different regions [but again I think
> total number is still zero].
>
>
>
> Please have a closer look in the pp.x input file [plot_num, nfile, weight
> ...] to see how you can do this. Also there are many similar issues from the
> past if you search the forum.
>
>
>
> Best,
>
>
>
> Hadi.
>
>
>
> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] 
> *On
> Behalf Of *Mudit Dixit
> *Sent:* 21 February 2014 13:28
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] Charge density with and without the electric
> field
>
>
>
> Dear Hadi Arefi,
>
> Thanks for the quick response.
>
> In the second point I meant that in the paper"
> http://www.nature.com/nature/journal/v488/n7413/full/nature11340.html";
> authors have calculated induced charge as
>
> 
>
> ?(G111,E=X)-?(G111,E=0).They have also shown the charge
> density difference plot in supporting information. I am unable
> to understand how they have obtained the induced charge as a number.
>
>
>
>
>
> Thank you so much for your help.
>
> Regards,
>
> Mudit Dixit
>
>
>
> On 21 February 2014 18:27, Hadi Arefi  wrote:
>
> Dear Mudit,
>
>
>
>
>
> >My questions are following:
>
> >1. How apply electric filed in 111 direction.
>
>
>
> You simply can redefine your lattice in the way that (111) direction lies
> along one of the x, y or z direction, then apply the field along that
> direction.
>
>
>
> >2. How
>
> 
>
> ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.
>
>
>
> Not quite sure what you mean but obviously the difference going to be an
> array which you can plot using xcrysden. My understanding is that you did
> not add external charge by applying electric field and the difference in
> charge density will rises from charge reorganisation due to external field
> (if there is any) unless you are interested in the local differences. Then
> you have the 3D mesh and need to find your points and subtract the values
> of equivalent points with and without applying field and then summation.
>
>
>
> HTH,
>
>
>
>
>
> Hadi Arefi
>
> PhD student
>
> Electronic theory&modeling group
>
> *Tyndall National Institute*
>
> University College Cork
>
> Lee Maltings
>
> Dyke Parade
>
> Cork, Ireland
>
> Tel: +353 21 234 6972
>
> Email: *hadi.arefi at tyndall.ie *
>
> Website: http://www.tyndall.ie
>
> [image: cid:image001.jpg at 01CBEADB.24D1AE90] <http://www.tyndall.ie/>
>
>
>
> .
>
>
>
>
>
> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] 
> *On
> Behalf Of *Mudit Dixit
> *Sent:* 20 February 2014 09:11
> *To:* pw_forum at pwscf.org
> *Subject:* [Pw_forum] Charge density with and without the electric field
>
>
>
> Dear PW users,
>
> I am trying to calculate charge density difference (i.e. induced charge)
> in presence of Electric Field(G111 direction) and absence of electric
> filed.
>
>
>
> My questions are following:
>
> 1. How apply electric filed in 111 direction.
>
> 2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.
>
>
>
> Thanks a lot for your help.
>
>
>
>
>
> Regards,
>
> Mudit
>
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Charge density with and without the electric field

[Mudit Dixit]

Dear Hadi Arefi,
??Thanks for the quick response.
In the second point I meant that in the paper"
http://www.nature.com/nature/journal/v488/n7413/full/nature11340.html";
authors have calculated induced charge as
?
?(G111,E=X)-?(G111,E=0).They have also shown the charge
density difference plot in supporting information. I am unable
to understand how they have obtained the induced charge as a number.


?Thank you so much for your help.
Regards,
Mudit Dixit?


On 21 February 2014 18:27, Hadi Arefi  wrote:

>  Dear Mudit,
>
>
>
>
>
> >My questions are following:
>
> >1. How apply electric filed in 111 direction.
>
>
>
> You simply can redefine your lattice in the way that (111) direction lies
> along one of the x, y or z direction, then apply the field along that
> direction.
>
>
>
> >2. How
> ??
> ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.
>
>
>
> Not quite sure what you mean but obviously the difference going to be an
> array which you can plot using xcrysden. My understanding is that you did
> not add external charge by applying electric field and the difference in
> charge density will rises from charge reorganisation due to external field
> (if there is any) unless you are interested in the local differences. Then
> you have the 3D mesh and need to find your points and subtract the values
> of equivalent points with and without applying field and then summation.
>
>
>
> HTH,
>
>
>
>
>
> Hadi Arefi
>
> PhD student
>
> Electronic theory&modeling group
>
> *Tyndall National Institute*
>
> University College Cork
>
> Lee Maltings
>
> Dyke Parade
>
> Cork, Ireland
>
> Tel: +353 21 234 6972
>
> Email: *hadi.arefi at tyndall.ie *
>
> Website: http://www.tyndall.ie
>
> [image: cid:image001.jpg at 01CBEADB.24D1AE90] <http://www.tyndall.ie/>
>
>
>
> .
>
>
>
>
>
> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] 
> *On
> Behalf Of *Mudit Dixit
> *Sent:* 20 February 2014 09:11
> *To:* pw_forum at pwscf.org
> *Subject:* [Pw_forum] Charge density with and without the electric field
>
>
>
> Dear PW users,
>
> I am trying to calculate charge density difference (i.e. induced charge)
> in presence of Electric Field(G111 direction) and absence of electric
> filed.
>
>
>
> My questions are following:
>
> 1. How apply electric filed in 111 direction.
>
> 2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.
>
>
>
> Thanks a lot for your help.
>
>
>
>
>
> Regards,
>
> Mudit
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] Charge density with and without the electric field

[Hadi Arefi]

Dear Mudit,

I couldn?t find a ?charge density difference plot? in supplementary information 
but I assume they just calculated the charge density for those two structures 
that you mentioned, and subtracted from each other. The result can be plotted 
as a distribution of charge in 3D (2D) or you can add up the values to get a 
number for different regions [but again I think total number is still zero].

Please have a closer look in the pp.x input file [plot_num, nfile, weight ?] to 
see how you can do this. Also there are many similar issues from the past if 
you search the forum.

Best,

Hadi.

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On 
Behalf Of Mudit Dixit
Sent: 21 February 2014 13:28
To: PWSCF Forum
Subject: Re: [Pw_forum] Charge density with and without the electric field

Dear Hadi Arefi,
??Thanks for the quick response.
In the second point I meant that in the 
paper"http://www.nature.com/nature/journal/v488/n7413/full/nature11340.html"; 
authors have calculated induced charge as
?
?(G111,E=X)-?(G111,E=0).They have also shown the charge density difference plot 
in supporting information. I am unable to understand how they have obtained the 
induced charge as a number.


?Thank you so much for your help.
Regards,
Mudit Dixit?

On 21 February 2014 18:27, Hadi Arefi mailto:hadi.arefi at tyndall.ie>> wrote:
Dear Mudit,


>My questions are following:
>1. How apply electric filed in 111 direction.

You simply can redefine your lattice in the way that (111) direction lies along 
one of the x, y or z direction, then apply the field along that direction.

>2. How
??
?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.

Not quite sure what you mean but obviously the difference going to be an array 
which you can plot using xcrysden. My understanding is that you did not add 
external charge by applying electric field and the difference in charge density 
will rises from charge reorganisation due to external field (if there is any) 
unless you are interested in the local differences. Then you have the 3D mesh 
and need to find your points and subtract the values of equivalent points with 
and without applying field and then summation.

HTH,


Hadi Arefi
PhD student
Electronic theory&modeling group
Tyndall National Institute
University College Cork
Lee Maltings
Dyke Parade
Cork, Ireland
Tel: +353 21 234 6972
Email: hadi.arefi at tyndall.ie<mailto:hadi.arefi at tyndall.ie>
Website: http://www.tyndall.ie<http://www.tyndall.ie/>
[cid:image001.jpg at 01CBEADB.24D1AE90]<http://www.tyndall.ie/>

.


From: pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org> 
[mailto:pw_forum-bounces at pwscf.org<mailto:pw_forum-boun...@pwscf.org>] On 
Behalf Of Mudit Dixit
Sent: 20 February 2014 09:11
To: pw_forum at pwscf.org<mailto:pw_forum at pwscf.org>
Subject: [Pw_forum] Charge density with and without the electric field

Dear PW users,
I am trying to calculate charge density difference (i.e. induced charge) in 
presence of Electric Field(G111 direction) and absence of electric filed.

My questions are following:
1. How apply electric filed in 111 direction.
2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.

Thanks a lot for your help.


Regards,
Mudit




___
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[Pw_forum] Charge density with and without the electric field

[Hadi Arefi]

Dear Mudit,


>My questions are following:
>1. How apply electric filed in 111 direction.

You simply can redefine your lattice in the way that (111) direction lies along 
one of the x, y or z direction, then apply the field along that direction.

>2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.

Not quite sure what you mean but obviously the difference going to be an array 
which you can plot using xcrysden. My understanding is that you did not add 
external charge by applying electric field and the difference in charge density 
will rises from charge reorganisation due to external field (if there is any) 
unless you are interested in the local differences. Then you have the 3D mesh 
and need to find your points and subtract the values of equivalent points with 
and without applying field and then summation.

HTH,


Hadi Arefi
PhD student
Electronic theory&modeling group
Tyndall National Institute
University College Cork
Lee Maltings
Dyke Parade
Cork, Ireland
Tel: +353 21 234 6972
Email: hadi.arefi at tyndall.ie<mailto:hadi.arefi at tyndall.ie>
Website: http://www.tyndall.ie<http://www.tyndall.ie/>
[cid:image001.jpg at 01CBEADB.24D1AE90]<http://www.tyndall.ie/>

.


From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On 
Behalf Of Mudit Dixit
Sent: 20 February 2014 09:11
To: pw_forum at pwscf.org
Subject: [Pw_forum] Charge density with and without the electric field

Dear PW users,
I am trying to calculate charge density difference (i.e. induced charge) in 
presence of Electric Field(G111 direction) and absence of electric filed.

My questions are following:
1. How apply electric filed in 111 direction.
2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.

Thanks a lot for your help.


Regards,
Mudit



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[Pw_forum] Charge density with and without the electric field

[Mudit Dixit]

Dear PW users,
 I am trying to calculate charge density difference (i.e. induced charge)
in presence of Electric Field(G111 direction) and absence of electric
filed.

My questions are following:
1. How apply electric filed in 111 direction.
2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid.

Thanks a lot for your help.


Regards,
Mudit
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[Pw_forum] charge density cal

[ehsan targholi]

hi
Dear all
i want to obtain charge density of graphene sheet vs its potential. Do you
already have someone do it or any this like calculation? i attached one
picture of this calculate.




ehsan targholi

graduate student of iust
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[Pw_forum] charge density cal.

[ehsan targholi]

dear all
thanks for yours reply.I modified the input file & run again. the output is
attached.
is it normal termination or not?
after this calculation i run ./plotrho to give charge density image. but i
saw tihs error in terminal:



 At line 114 of file plotrho.f90 (unit = 5, file = 'stdin')
Fortran runtime error: Bad integer for item 3 in list input.



 and output of ./plotrho is :

Input file > r0   :   0.  0.  0.
tau1 :   1.  1.  0.
tau2 :   0.  0.  1.
read   2 atomic positions
output file > Read  56 * 40  grid
Logarithmic scale (y/n)? > Bounds: 0.0014110.087440
min, max, # of levels >

what i can do?


On Thu, Feb 6, 2014 at 1:49 AM, Thomas Brumme
wrote:

> As suggested in the error message you have to write
>
> &inputpp
>
> and not
>
> &Charges
>
> See also
>
> http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html
>
> Thomas
>
> ehsan targholi  a ?crit :
>
> > Excuse me . i now attach the file.
> >
> >
> > On Wed, Feb 5, 2014 at 11:08 PM, Hadi Arefi 
> wrote:
> >
> >>  Hi,
> >>
> >>
> >>
> >> Not quite sure but I think some parameter(s) has changed in the
> >> pp.inname list in recent version compare to old ones as it was
> >> discussed while
> >> ago in the forum. Better you just download the new example folder as
> well
> >> or modify it based on new changes.
> >>
> >> By the way I didn't get your attachment so I think nobody did.
> >>
> >>
> >>
> >> H.
> >>
> >>
> >>
> >>
> >>
> >> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at 
> >> pwscf.org]
> *On
> >> Behalf Of *ehsan targholi
> >> *Sent:* 05 February 2014 18:50
> >> *To:* PWSCF Forum
> >> *Subject:* Re: [Pw_forum] charge density cal.
> >>
> >>
> >>
> >> Dear all
> >>
> >> thanks a lot for your reply
> >>
> >> i use Example 5 of the QE-4.3.2 with espresso 5.3.2
> >>
> >> i attached my input file. pleas explore input file and guide me again.
> >>
> >>  best regard
> >>
> >> ehsan targholi
> >>
> >> graduate student of iust
> >>
> >>
> >>
> >> On Wed, Feb 5, 2014 at 9:06 PM, Manu Hegde  wrote:
> >>
> >> please give the input information as well!
> >>
> >>
> >>
> >> On Wed, Feb 5, 2014 at 11:43 AM, ehsan targholi 
> >> wrote:
> >>
> >>   hi
> >>
> >> espresso users
> >>
> >> i want to obtain the charge density of si in example 5. but when i use
> >> pp.x calculation with &inputpp namelist, after scf , give this error:
> >>
> >>
> >>
> >>
> >>
> %%
> >>
> >>  Error in routine postproc (1):
> >>
> >>  reading inputpp namelist
> >>
> >>
> >>
> >>
> %%
> >>
> >>
> >>
> >>  stopping ...
> >>
> >>  what is my mistake ?
> >>
> >>
> >>
> >>
> >>
> >> best regard
> >>
> >>
> >>
> >> ehsan targholi
> >>
> >> graduate student of iust
> >>
> >>
> >>
> >> ___
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >>
> >>
> >>
> >>
> >> ___
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >>
> >>
> >>
> >> ___
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >>
> >
>
>
>
> 
> This message was sent using IMP, the Internet Messaging Program.
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] charge density cal.

[ehsan targholi]

Excuse me . i now attach the file.


On Wed, Feb 5, 2014 at 11:08 PM, Hadi Arefi  wrote:

>  Hi,
>
>
>
> Not quite sure but I think some parameter(s) has changed in the pp.inname 
> list in recent version compare to old ones as it was discussed while
> ago in the forum. Better you just download the new example folder as well
> or modify it based on new changes.
>
> By the way I didn't get your attachment so I think nobody did.
>
>
>
> H.
>
>
>
>
>
> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] 
> *On
> Behalf Of *ehsan targholi
> *Sent:* 05 February 2014 18:50
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] charge density cal.
>
>
>
> Dear all
>
> thanks a lot for your reply
>
> i use Example 5 of the QE-4.3.2 with espresso 5.3.2
>
> i attached my input file. pleas explore input file and guide me again.
>
>  best regard
>
> ehsan targholi
>
> graduate student of iust
>
>
>
> On Wed, Feb 5, 2014 at 9:06 PM, Manu Hegde  wrote:
>
> please give the input information as well!
>
>
>
> On Wed, Feb 5, 2014 at 11:43 AM, ehsan targholi 
> wrote:
>
>   hi
>
> espresso users
>
> i want to obtain the charge density of si in example 5. but when i use
> pp.x calculation with &inputpp namelist, after scf , give this error:
>
>
>
>
> %%
>
>  Error in routine postproc (1):
>
>  reading inputpp namelist
>
>
>  
> %%
>
>
>
>  stopping ...
>
>  what is my mistake ?
>
>
>
>
>
> best regard
>
>
>
> ehsan targholi
>
> graduate student of iust
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] charge density cal.

[Thomas Brumme]

As suggested in the error message you have to write

&inputpp

and not

&Charges

See also

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html

Thomas

ehsan targholi  a ?crit?:

> Excuse me . i now attach the file.
>
>
> On Wed, Feb 5, 2014 at 11:08 PM, Hadi Arefi  wrote:
>
>>  Hi,
>>
>>
>>
>> Not quite sure but I think some parameter(s) has changed in the  
>> pp.inname list in recent version compare to old ones as it was  
>> discussed while
>> ago in the forum. Better you just download the new example folder as well
>> or modify it based on new changes.
>>
>> By the way I didn't get your attachment so I think nobody did.
>>
>>
>>
>> H.
>>
>>
>>
>>
>>
>> *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] 
>> *On
>> Behalf Of *ehsan targholi
>> *Sent:* 05 February 2014 18:50
>> *To:* PWSCF Forum
>> *Subject:* Re: [Pw_forum] charge density cal.
>>
>>
>>
>> Dear all
>>
>> thanks a lot for your reply
>>
>> i use Example 5 of the QE-4.3.2 with espresso 5.3.2
>>
>> i attached my input file. pleas explore input file and guide me again.
>>
>>  best regard
>>
>> ehsan targholi
>>
>> graduate student of iust
>>
>>
>>
>> On Wed, Feb 5, 2014 at 9:06 PM, Manu Hegde  wrote:
>>
>> please give the input information as well!
>>
>>
>>
>> On Wed, Feb 5, 2014 at 11:43 AM, ehsan targholi 
>> wrote:
>>
>>   hi
>>
>> espresso users
>>
>> i want to obtain the charge density of si in example 5. but when i use
>> pp.x calculation with &inputpp namelist, after scf , give this error:
>>
>>
>>
>>
>> %%
>>
>>  Error in routine postproc (1):
>>
>>  reading inputpp namelist
>>
>>
>>   
>> %%
>>
>>
>>
>>  stopping ...
>>
>>  what is my mistake ?
>>
>>
>>
>>
>>
>> best regard
>>
>>
>>
>> ehsan targholi
>>
>> graduate student of iust
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>




This message was sent using IMP, the Internet Messaging Program.

[Pw_forum] charge density cal.

[ehsan targholi]

Dear all
thanks a lot for your reply
i use Example 5 of the QE-4.3.2 with espresso 5.3.2
i attached my input file. pleas explore input file and guide me again.


best regard
ehsan targholi
graduate student of iust


On Wed, Feb 5, 2014 at 9:06 PM, Manu Hegde  wrote:

> please give the input information as well!
>
>
> On Wed, Feb 5, 2014 at 11:43 AM, ehsan targholi wrote:
>
>> hi
>> espresso users
>> i want to obtain the charge density of si in example 5. but when i use
>> pp.x calculation with &inputpp namelist, after scf , give this error:
>>
>>
>> %%
>>  Error in routine postproc (1):
>>  reading inputpp namelist
>>
>>  
>> %%
>>
>>  stopping ...
>>  what is my mistake ?
>>
>>
>> best regard
>>
>> ehsan targholi
>> graduate student of iust
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] charge density cal.

[ehsan targholi]

hi
espresso users
i want to obtain the charge density of si in example 5. but when i use pp.x
calculation with &inputpp namelist, after scf , give this error:

%%
 Error in routine postproc (1):
 reading inputpp namelist
 %%

 stopping ...
 what is my mistake ?


best regard

ehsan targholi
graduate student of iust
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[Pw_forum] charge density cal.

[Hadi Arefi]

Hi,

Not quite sure but I think some parameter(s) has changed in the pp.in name list 
in recent version compare to old ones as it was discussed while ago in the 
forum. Better you just download the new example folder as well or modify it 
based on new changes.
By the way I didn't get your attachment so I think nobody did.

H.


From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On 
Behalf Of ehsan targholi
Sent: 05 February 2014 18:50
To: PWSCF Forum
Subject: Re: [Pw_forum] charge density cal.

Dear all
thanks a lot for your reply
i use Example 5 of the QE-4.3.2 with espresso 5.3.2
i attached my input file. pleas explore input file and guide me again.

best regard
ehsan targholi
graduate student of iust

On Wed, Feb 5, 2014 at 9:06 PM, Manu Hegde mailto:mhegde at uwaterloo.ca>> wrote:
please give the input information as well!

On Wed, Feb 5, 2014 at 11:43 AM, ehsan targholi mailto:targholi at gmail.com>> wrote:
hi
espresso users
i want to obtain the charge density of si in example 5. but when i use pp.x 
calculation with &inputpp namelist, after scf , give this error:

%%
 Error in routine postproc (1):
 reading inputpp namelist
 %%

 stopping ...
 what is my mistake ?


best regard

ehsan targholi
graduate student of iust

___
Pw_forum mailing list
Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
http://pwscf.org/mailman/listinfo/pw_forum


___
Pw_forum mailing list
Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
http://pwscf.org/mailman/listinfo/pw_forum

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[Pw_forum] charge density cal.

[Thomas Brumme]

Dear Ehsan,

which example 5?
Example 5 of the QE-5.0.2 PW, is a calculation of isolated O and Al atoms.
Example 5 of the QE-5.0.2 PP, is a calculation using LDA+U

Example 5 of the QE-4.3.2 is the example of Si...
However, I guess that you are using the QE-5.0.2... Maybe something changed?

Do you use the "run_example" script?

Thomas


On 02/05/2014 05:43 PM, ehsan targholi wrote:
> hi
> espresso users
> i want to obtain the charge density of si in example 5. but when i use 
> pp.x calculation with &inputpp namelist, after scf , give this error:
>
> %%
>  Error in routine postproc (1):
>  reading inputpp namelist
>  
> %%
>
>  stopping ...
>  what is my mistake ?
>
>
> best regard
>
> ehsan targholi
> graduate student of iust
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Dr. rer. nat. Thomas Brumme
Institut de Min?ralogie, de Physique des Mat?riaux, et de Cosmochimie
Sorbonne Universit?s - UPMC Univ Paris 06
4 Place Jussieu
75005 Paris

Tel:  +33 (0) 1 442 77204

email: Thomas.Brumme at impmc.upmc.fr

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[Pw_forum] charge density cal.

[Hadi Arefi]

Dear Ehsan,

As it clearly says, there is something wrong with the input parameters you of 
pp.in.
For more help you need to provide your input file/files description.

H.

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On 
Behalf Of ehsan targholi
Sent: 05 February 2014 16:43
To: PWSCF Forum
Subject: [Pw_forum] charge density cal.

hi
espresso users
i want to obtain the charge density of si in example 5. but when i use pp.x 
calculation with &inputpp namelist, after scf , give this error:

%%
 Error in routine postproc (1):
 reading inputpp namelist
 %%

 stopping ...
 what is my mistake ?


best regard

ehsan targholi
graduate student of iust
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[Pw_forum] charge density cal.

[Manu Hegde]

please give the input information as well!


On Wed, Feb 5, 2014 at 11:43 AM, ehsan targholi  wrote:

> hi
> espresso users
> i want to obtain the charge density of si in example 5. but when i use
> pp.x calculation with &inputpp namelist, after scf , give this error:
>
>
> %%
>  Error in routine postproc (1):
>  reading inputpp namelist
>
>  
> %%
>
>  stopping ...
>  what is my mistake ?
>
>
> best regard
>
> ehsan targholi
> graduate student of iust
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Charge density at any k-point in the Brillouin zone

[Lorenzo Paulatto]

On 05/04/2013 07:37 AM, koushik pal wrote:

> I am not sure about *"kpoint=1"* because in the scf output file 
> "kpoint=1" means the \Gamma point.
>
If you use an automatically-generated NON-SHIFTED grid, than the Gamma 
point is normally the first one in the list.

But I cannot be sure either: I have not seen your input nor your output 
file.


best regards

-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
phone:+33 (0)1 44275 084 / skype: paulatz
www:  http://www-int.impmc.upmc.fr/~paulatto/
mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 5

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[Pw_forum] Charge density at any k-point in the Brillouin zone

[xirainbow]

Dear Koushik:
   In the following website, I gave an example of graphene
nano-ribbon. I hope it is useful to you   ??
http://blog.sina.com.cn/s/blog_5f15ead20100d3wp.html

On Sat, May 4, 2013 at 1:37 PM, koushik pal
wrote:

> Dear Prof. Paulatto,
> I want to know one more thing about charge density visualization. If I
> have understood properly your answer , to visualize the contribution from a
> specific point "k" and band "n", which is the square modulus of the
> wavefunction
> \psi_{k,n}, first I have to do a scf calculation on a regular k-mesh,
> secondly I have to do a nscf calculation at that particular "kpoint" in the
> BZ and then I have to run pp.x  with "plot_num =7" and "*kpoint =1" (is
> this correct?*).
> I am not sure about *"kpoint=1"* because in the scf output file
> "kpoint=1" means the \Gamma point.
>
> Thanks a lot.
>
> With Regards,
> Koushik
> MS student
> JNCASR
> Bangalore-560064
> India
>
>
> > Dear PW users,
> > I need some clarifications on the input file of pp.x. In the &inputpp
> > namelist, what does the "kpoint" mean?
> > To be specific, If I want to visualize the charge density of a
> > particular band ("kband") at any arbitrary k-point in the Brillouin
> > zone (e.g at Gamma (0, 0, 0) and Z(0, 0, 0.5)) what "kpoint" (integer)
> > values should I specify  in each case in the &inputpp namelist?
> > Thanks in advance.
> Dear Koushik,
> the charge density is obtained after a sum over the occupied k-points
> and bands, so you cannot print it for a single k-point.
>
> On the other hand, you can plot the contribution from a specific point
> "k" and band "n", which is the square modulus of the wavefunction
> \psi_{k,n}.
>
> The value of "kpoint" in &inputpp is the index of the k-point, as listed
> in the output of pw.x. If you want to plot a specific point that is not
> in the list you will have to do a nscf calculation first.
>
> best regards
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
> -- *
> *
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 

Hui Wang
School of physics, Fudan University, Shanghai, China
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[Pw_forum] Charge density at any k-point in the Brillouin zone

[koushik pal]

Dear Prof. Paulatto,
I want to know one more thing about charge density visualization. If I have
understood properly your answer , to visualize the contribution from a
specific point "k" and band "n", which is the square modulus of the
wavefunction
\psi_{k,n}, first I have to do a scf calculation on a regular k-mesh,
secondly I have to do a nscf calculation at that particular "kpoint" in the
BZ and then I have to run pp.x  with "plot_num =7" and "*kpoint =1" (is
this correct?*).
I am not sure about *"kpoint=1"* because in the scf output file "kpoint=1"
means the \Gamma point.

Thanks a lot.

With Regards,
Koushik
MS student
JNCASR
Bangalore-560064
India


> Dear PW users,
> I need some clarifications on the input file of pp.x. In the &inputpp
> namelist, what does the "kpoint" mean?
> To be specific, If I want to visualize the charge density of a
> particular band ("kband") at any arbitrary k-point in the Brillouin
> zone (e.g at Gamma (0, 0, 0) and Z(0, 0, 0.5)) what "kpoint" (integer)
> values should I specify  in each case in the &inputpp namelist?
> Thanks in advance.
Dear Koushik,
the charge density is obtained after a sum over the occupied k-points
and bands, so you cannot print it for a single k-point.

On the other hand, you can plot the contribution from a specific point
"k" and band "n", which is the square modulus of the wavefunction
\psi_{k,n}.

The value of "kpoint" in &inputpp is the index of the k-point, as listed
in the output of pw.x. If you want to plot a specific point that is not
in the list you will have to do a nscf calculation first.

best regards

--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
-- *
*
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[Pw_forum] Charge density at any k-point in the Brillouin

[koushik pal]

Thanks Prof. Paulatto and Prof. Giannozzi for the clarification.

With Regards,
Koushik
JNCASR
Bangalore-560064
>
> Dear PW users,
> I need some clarifications on the input file of pp.x. In the &inputpp
> namelist, what does the "kpoint" mean?
> To be specific, If I want to visualize the charge density of a
> particular band ("kband") at any arbitrary k-point in the Brillouin
> zone (e.g at Gamma (0, 0, 0) and Z(0, 0, 0.5)) what "kpoint" (integer)
> values should I specify  in each case in the &inputpp namelist?
> Thanks in advance.
Dear Koushik,
the charge density is obtained after a sum over the occupied k-points
and bands, so you cannot print it for a single k-point.

On the other hand, you can plot the contribution from a specific point
"k" and band "n", which is the square modulus of the wavefunction
\psi_{k,n}.

The value of "kpoint" in &inputpp is the index of the k-point, as listed
in the output of pw.x. If you want to plot a specific point that is not
in the list you will have to do a nscf calculation first.

best regards

--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05



------

Message: 5
Date: Thu, 02 May 2013 15:47:01 +0200
From: Paolo Giannozzi 
Subject: Re: [Pw_forum] Charge density at any k-point in the Brillouin
zone
To: PWSCF Forum 
Message-ID: <1367502421.5282.1.camel at fe12lx.fisica.uniud.it>
Content-Type: text/plain; charset="UTF-8"

On Thu, 2013-05-02 at 18:27 +0530, koushik pal wrote:

> To be specific, If I want to visualize the charge density of a
> particular band ("kband") at any arbitrary k-point in the Brillouin
> zone (e.g at Gamma (0, 0, 0) and Z(0, 0, 0.5)) what "kpoint" (integer)
> values should I specify  in each case in the &inputpp namelist?

kpoint is the index of k-points as they appear in the output of pw.x

P.

--
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222
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[Pw_forum] Charge density at any k-point in the Brillouin zone

[koushik pal]

Dear PW users,
I need some clarifications on the input file of pp.x. In the &inputpp
namelist, what does the "kpoint" mean?
To be specific, If I want to visualize the charge density of a particular
band ("kband") at any arbitrary k-point in the Brillouin zone (e.g at Gamma
(0, 0, 0) and Z(0, 0, 0.5)) what "kpoint" (integer) values should I
specify  in each case in the &inputpp namelist?
Thanks in advance.

Regards,
Koushik
MS student
JNCASR, Bangalore-560064
India
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[Pw_forum] Charge density at any k-point in the Brillouin zone

[Paolo Giannozzi]

On Thu, 2013-05-02 at 18:27 +0530, koushik pal wrote:

> To be specific, If I want to visualize the charge density of a
> particular band ("kband") at any arbitrary k-point in the Brillouin
> zone (e.g at Gamma (0, 0, 0) and Z(0, 0, 0.5)) what "kpoint" (integer)
> values should I specify  in each case in the &inputpp namelist? 

kpoint is the index of k-points as they appear in the output of pw.x

P.

-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] Charge density at any k-point in the Brillouin zone

[Lorenzo Paulatto]

On 05/02/2013 02:57 PM, koushik pal wrote:
>
>
> Dear PW users,
> I need some clarifications on the input file of pp.x. In the &inputpp 
> namelist, what does the "kpoint" mean?
> To be specific, If I want to visualize the charge density of a 
> particular band ("kband") at any arbitrary k-point in the Brillouin 
> zone (e.g at Gamma (0, 0, 0) and Z(0, 0, 0.5)) what "kpoint" (integer) 
> values should I specify  in each case in the &inputpp namelist?
> Thanks in advance.
Dear Koushik,
the charge density is obtained after a sum over the occupied k-points 
and bands, so you cannot print it for a single k-point.

On the other hand, you can plot the contribution from a specific point 
"k" and band "n", which is the square modulus of the wavefunction 
\psi_{k,n}.

The value of "kpoint" in &inputpp is the index of the k-point, as listed 
in the output of pw.x. If you want to plot a specific point that is not 
in the list you will have to do a nscf calculation first.

best regards

-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

[Pw_forum] charge density in real space

[Bramha Pandey]

PW forum itself is a good link to find out the answers or closer to the
matters.
Please search in it as Prof. Axel has said before.
Can you please give your affiliation in this forum.


On Wed, Apr 17, 2013 at 3:58 PM, shruti shukla
wrote:

> Dear Axel,
>
> Thanks for instant reply. can you please give the link.
>
>   at Middle?>
> Get your own *FREE* website and domain with business email solutions, click
> here
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Thanks and Regards
Bramha Prasad Pandey
Indian School of Mines(ISM)
Dhanbad, INDIA.
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[Pw_forum] charge density in real space

[Imam Mighfar]

Dear Shruti, you can look into example05 in the QE distribution. The
description of relevant input variables is in the espresso/Doc/PP or
espresso/PP/Doc. Here's the link for your ease:
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html

Hope it helps.

-- 
Mighfar Imam,
Postdoctoral Fellow,
The Abdus Salam International Centre
for Theoretical Physics (ICTP)
Strada Costiera, 11
I-34151 Trieste, Italy.
Mobile: +393349389285
Office: (+39) 040 2240 459

> Dear Axel,
>
> Thanks for instant reply. can you please give the
> link.___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] charge density in real space

[Axel Kohlmeyer]

On Wed, Apr 17, 2013 at 10:16 AM, shruti shukla  wrote:

> Dear Users,
>
> I am studying a layered heterostructure. I want to see the charge density
> at the interface. Is it posiible to obtain charge density in real space
> using PWSCF. I am a beginner in PWSCF so your help will be usefull.


as a beginner you should start by reading through the documentation and
checking out the existing tutorial material and you will magically find
many of your questions - like this one - already answered (usually
positively, too).

axel.


>

Thanks,
>
> Shruti Tiwari
>
>   at Middle?>
> Get your own *FREE* website and domain with business email solutions, click
> here
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
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[Pw_forum] charge density in real space

[shruti shukla]

Dear Axel,

Thanks for instant reply. can you please give the link.
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[Pw_forum] charge density in real space

[shruti shukla]

Dear Users,

I am studying a layered heterostructure. I want to see the charge density at 
the interface. Is it posiible to obtain charge density in real space using 
PWSCF. I am a beginner in PWSCF so your help will be usefull.
Thanks,

Shruti Tiwari
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[Pw_forum] charge density data in pp.x

[Paolo Giannozzi]

On Wed, 2013-02-27 at 16:54 -0500, Ruibin Liu wrote:

> Thanks for replying. X.rho.dat refers to the generated charge density
> file for X.

who is X?

>  For the first question, do you mean that if I set 'fast3d' to .false.
> and recompile it, the code will perform interpolation?

I mean that if you look how it is defined, you understand how it works.
Do not forget that interpolation on a 3d grid is extremely slow if done
via (slow) Fourier transform

P.
> 
> Best,
> Ruibin
> 
> On Wed, Feb 27, 2013 at 4:21 PM, Paolo Giannozzi
>  wrote:
> On Tuesday 26 February 2013 22:52, Ruibin Liu wrote:
> 
> > In pp.x, if plot_num=0, we can get the total charge density
> data, and if we
> > set output_format to be 3, it seems that we can also set the
> density of
> >  meshgrid as described by the Document for PP. However,
> whatever I change
> > the nx, ny and nz numbers to be, the density of meshgrid
> won't change.
> 
> 
> the code performs interpolation in three dimensions only if
> there is
> no other possibility. See variable "fast3d" in
> PP/src/hdens.f90. If it is
> set to .true., the original FFT mesh is used.
> 
> > Another question is how the charge density data is arrayed
> in the
> > X.rho.dat?
> 
> 
> which file are you referring to?
> 
> --
> Paolo Giannozzi, IOM-Democritos and DCFA, UniUD
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
> 
> 
> 
> 
> -- 
> Liu, Ruibin
> Department of Chemistry
> 
> Duke University
> Durham, NC, 27708
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

[Pw_forum] charge density data in pp.x

[Ruibin Liu]

If the system is Cd6Se6, then X is Cd6Se6. X refers to the calculated
particle/molecule.

On Thu, Feb 28, 2013 at 10:35 AM, Paolo Giannozzi wrote:

> On Wed, 2013-02-27 at 16:54 -0500, Ruibin Liu wrote:
>
> > Thanks for replying. X.rho.dat refers to the generated charge density
> > file for X.
>
> who is X?
>
> >  For the first question, do you mean that if I set 'fast3d' to .false.
> > and recompile it, the code will perform interpolation?
>
> I mean that if you look how it is defined, you understand how it works.
> Do not forget that interpolation on a 3d grid is extremely slow if done
> via (slow) Fourier transform
>
> P.
> >
> > Best,
> > Ruibin
> >
> > On Wed, Feb 27, 2013 at 4:21 PM, Paolo Giannozzi
> >  wrote:
> > On Tuesday 26 February 2013 22:52, Ruibin Liu wrote:
> >
> > > In pp.x, if plot_num=0, we can get the total charge density
> > data, and if we
> > > set output_format to be 3, it seems that we can also set the
> > density of
> > >  meshgrid as described by the Document for PP. However,
> > whatever I change
> > > the nx, ny and nz numbers to be, the density of meshgrid
> > won't change.
> >
> >
> > the code performs interpolation in three dimensions only if
> > there is
> > no other possibility. See variable "fast3d" in
> > PP/src/hdens.f90. If it is
> > set to .true., the original FFT mesh is used.
> >
> > > Another question is how the charge density data is arrayed
> > in the
> > > X.rho.dat?
> >
> >
> > which file are you referring to?
> >
> > --
> > Paolo Giannozzi, IOM-Democritos and DCFA, UniUD
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> > Liu, Ruibin
> > Department of Chemistry
> >
> > Duke University
> > Durham, NC, 27708
> >
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
*Liu, Ruibin*
Department of Chemistry
Duke University
Durham, NC, 27708
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[Pw_forum] charge density data in pp.x

[Paolo Giannozzi]

On Tuesday 26 February 2013 22:52, Ruibin Liu wrote:

> In pp.x, if plot_num=0, we can get the total charge density data, and if we
> set output_format to be 3, it seems that we can also set the density of
>  meshgrid as described by the Document for PP. However, whatever I change
> the nx, ny and nz numbers to be, the density of meshgrid won't change.

the code performs interpolation in three dimensions only if there is
no other possibility. See variable "fast3d" in PP/src/hdens.f90. If it is
set to .true., the original FFT mesh is used.

> Another question is how the charge density data is arrayed in the
> X.rho.dat?

which file are you referring to?

--
Paolo Giannozzi, IOM-Democritos and DCFA, UniUD

[Pw_forum] charge density data in pp.x

[Ruibin Liu]

Thanks for replying. X.rho.dat refers to the generated charge density file
for X. For the first question, do you mean that if I set 'fast3d' to
.false. and recompile it, the code will perform interpolation?

Best,
Ruibin

On Wed, Feb 27, 2013 at 4:21 PM, Paolo Giannozzi wrote:

> On Tuesday 26 February 2013 22:52, Ruibin Liu wrote:
>
> > In pp.x, if plot_num=0, we can get the total charge density data, and if
> we
> > set output_format to be 3, it seems that we can also set the density of
> >  meshgrid as described by the Document for PP. However, whatever I change
> > the nx, ny and nz numbers to be, the density of meshgrid won't change.
>
> the code performs interpolation in three dimensions only if there is
> no other possibility. See variable "fast3d" in PP/src/hdens.f90. If it is
> set to .true., the original FFT mesh is used.
>
> > Another question is how the charge density data is arrayed in the
> > X.rho.dat?
>
> which file are you referring to?
>
> --
> Paolo Giannozzi, IOM-Democritos and DCFA, UniUD
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
*Liu, Ruibin*
Department of Chemistry
Duke University
Durham, NC, 27708
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[Pw_forum] charge density data in pp.x

[Ruibin Liu]

Does anyone know about it?

On Tue, Feb 26, 2013 at 4:52 PM, Ruibin Liu  wrote:

> Hi all,
>
> In pp.x, if plot_num=0, we can get the total charge density data, and if
> we set output_format to be 3, it seems that we can also set the density of
>  meshgrid as described by the Document for PP. However, whatever I change
> the nx, ny and nz numbers to be, the density of meshgrid won't change. Does
> anyone know the reasons and how to change the density of meshgrid?
>
> Another question is how the charge density data is arrayed in the
> X.rho.dat? Or in other words, are they cycling in x, y, z order?
>
>
> Best,
> Ruibin
> --
> *Liu, Ruibin*
> Department of Chemistry
> Duke University
> Durham, NC, 27708
>
>


-- 
*Liu, Ruibin*
Department of Chemistry
Duke University
Durham, NC, 27708
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[Pw_forum] charge density data in pp.x

[Ruibin Liu]

Hi all,

In pp.x, if plot_num=0, we can get the total charge density data, and if we
set output_format to be 3, it seems that we can also set the density of
 meshgrid as described by the Document for PP. However, whatever I change
the nx, ny and nz numbers to be, the density of meshgrid won't change. Does
anyone know the reasons and how to change the density of meshgrid?

Another question is how the charge density data is arrayed in the
X.rho.dat? Or in other words, are they cycling in x, y, z order?


Best,
Ruibin
-- 
*Liu, Ruibin*
Department of Chemistry
Duke University
Durham, NC, 27708
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[Pw_forum] charge density with denser grid and wrong cube file

[Paolo Giannozzi]

On Feb 19, 2013, at 13:23 , Thomas Gruber wrote:

> I can note find the  "voronoy.f90".

it is present only in older versions

> When using nx,ny,nz for a plane oder orthorhombic box,
> is it also an interpolation in real space?

no, it is done in G-space and takes approximately forever.
>


P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] charge density with denser grid and wrong cube file

[Thomas Gruber]

> Not sure what the problem with the "cube" file is.
> FFT arrays obey periodic boundary conditions: the
> index runs from 1 to nr, and f(nr+1) =>  f(1) . Is
> this the problem?
Yes this is the problem. In the cube file the last data point should be 
the same like the first one (cell boundry), as it is implemented in for 
the xsf file. Just adding the first data point along each direction an 
the end to get a grid that is +1 in each direction.
>
> About the denser grid: I don't think it is that simple.
> Either you perform a Fourier interpolation (have a look
> at code "voronoy.f90" in v.4.1.3) or you perform a local
> interpolation in real space.
I can note find the  "voronoy.f90". When using nx,ny,nz for a plane oder 
orthorhombic box, is it also an interpolation in real space? 
("Otherwise, the required 3D grid is generated from the Fourier 
components (may be VERY slow)" from the pp.x documentation) Can these 
parameters be used to calculate a data grid that is denser than the FFT 
grid? It is ok if it is a multiple of the FFT grid.
> P.
>
> On Mon, 2013-02-18 at 16:56 +0100, Thomas Gruber wrote:
>> >  Hallo all,
>> >  
>> >  I have two problems:
>> >  1. I like to have the charge_density.xsf/*.cube with output_format=5/6,
>> >  but with a denser grid than the FFT grid. nx,ny,nz are ignored in this
>> >  case. They work for output_format=3 with an orthorhombic box, but I want
>> >  my unit cell.
>> >  
>> >  2. The output format for *.xsf works fine, but not for *.cube. For xsf
>> >  the data_grid is x+1,y+1,z+1, but not for cube (x,y,z). The *.cube also
>> >  needs x+1,y+1,z+1 to get the write volume, atom positions and no offset
>> >  along the unit cell surface for the charge density. I tried to correct
>> >  the cube.f90 in PP but the charge density data is still not correct. I
>> >  increased nr# by 1 in each case:
>> >  
>> >  WRITE(ounit,*) 'Cubfile created from PWScf calculation'
>> >  WRITE(ounit,*) ' Total SCF Density'
>> >  !origin is forced to (0.0,0.0,0.0)
>> >  WRITE(ounit,'(I5,3F12.6)') nat, 0.0d0, 0.0d0, 0.0d0
>> >  WRITE(ounit,'(I5,3F12.6)') nr1+1, (alat*at(i,1)/dble(nr1),i=1,3)
>> >  WRITE(ounit,'(I5,3F12.6)') nr2+1, (alat*at(i,2)/dble(nr2),i=1,3)
>> >  WRITE(ounit,'(I5,3F12.6)') nr3+1, (alat*at(i,3)/dble(nr3),i=1,3)
>> >  
>> >  DO i=1,nat
>> > nt = ityp(i)
>> > ! find atomic number for this atom.
>> > at_num = atomic_number(trim(atm(nt)))
>> > at_chrg= dble(at_num)
>> > ! at_chrg could be alternatively set to valence charge
>> > ! positions are in cartesian coordinates and a.u.
>> > !
>> > ! wrap coordinates back into cell.
>> > tpos = matmul( transpose(bg), tau(:,i) )
>> > tpos = tpos - nint(tpos - 0.5d0)
>> > inpos = alat * matmul( at, tpos )
>> > WRITE(ounit,'(I5,5F12.6)') at_num, at_chrg, inpos
>> >  ENDDO
>> >  
>> >  DO i1=1,nr1+1
>> > DO i2=1,nr2+1
>> >WRITE(ounit,'(6E13.5)') (rho(i1,i2,i3),i3=1,nr3+1)
>> > ENDDO
>> >  ENDDO
>> >  
>> >  Can someone give me the correction for cube.f90 and a way to increase
>> >  the data_grid density for the output_format=5/6?
>> >  
>> >  Sincerely,
>> >  
>> >  Thomas Gruber
>> >  
> -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

Sincerely,

Thomas Gruber

-- 
Thomas Gruber
Institut f?r Theoretische Physik
TU Bergakademie Freiberg
Leipziger Str. 23, 09599 Freiberg, Germany
Tel: +49 (0)3731 392006
Email: thomas.gruber at physik.tu-freiberg.de

[Pw_forum] charge density with denser grid and wrong cube file

[Paolo Giannozzi]

Not sure what the problem with the "cube" file is.
FFT arrays obey periodic boundary conditions: the
index runs from 1 to nr, and f(nr+1) => f(1) . Is
this the problem?

About the denser grid: I don't think it is that simple.
Either you perform a Fourier interpolation (have a look 
at code "voronoy.f90" in v.4.1.3) or you perform a local 
interpolation in real space.

P.

On Mon, 2013-02-18 at 16:56 +0100, Thomas Gruber wrote:
> Hallo all,
> 
> I have two problems:
> 1. I like to have the charge_density.xsf/*.cube with output_format=5/6, 
> but with a denser grid than the FFT grid. nx,ny,nz are ignored in this 
> case. They work for output_format=3 with an orthorhombic box, but I want 
> my unit cell.
> 
> 2. The output format for *.xsf works fine, but not for *.cube. For xsf 
> the data_grid is x+1,y+1,z+1, but not for cube (x,y,z). The *.cube also 
> needs x+1,y+1,z+1 to get the write volume, atom positions and no offset 
> along the unit cell surface for the charge density. I tried to correct 
> the cube.f90 in PP but the charge density data is still not correct. I 
> increased nr# by 1 in each case:
> 
>WRITE(ounit,*) 'Cubfile created from PWScf calculation'
>WRITE(ounit,*) ' Total SCF Density'
> !origin is forced to (0.0,0.0,0.0)
>WRITE(ounit,'(I5,3F12.6)') nat, 0.0d0, 0.0d0, 0.0d0
>WRITE(ounit,'(I5,3F12.6)') nr1+1, (alat*at(i,1)/dble(nr1),i=1,3)
>WRITE(ounit,'(I5,3F12.6)') nr2+1, (alat*at(i,2)/dble(nr2),i=1,3)
>WRITE(ounit,'(I5,3F12.6)') nr3+1, (alat*at(i,3)/dble(nr3),i=1,3)
> 
>DO i=1,nat
>   nt = ityp(i)
>   ! find atomic number for this atom.
>   at_num = atomic_number(trim(atm(nt)))
>   at_chrg= dble(at_num)
>   ! at_chrg could be alternatively set to valence charge
>   ! positions are in cartesian coordinates and a.u.
>   !
>   ! wrap coordinates back into cell.
>   tpos = matmul( transpose(bg), tau(:,i) )
>   tpos = tpos - nint(tpos - 0.5d0)
>   inpos = alat * matmul( at, tpos )
>   WRITE(ounit,'(I5,5F12.6)') at_num, at_chrg, inpos
>ENDDO
> 
>DO i1=1,nr1+1
>   DO i2=1,nr2+1
>  WRITE(ounit,'(6E13.5)') (rho(i1,i2,i3),i3=1,nr3+1)
>   ENDDO
>ENDDO
> 
> Can someone give me the correction for cube.f90 and a way to increase 
> the data_grid density for the output_format=5/6?
> 
> Sincerely,
> 
> Thomas Gruber
> 

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

[Pw_forum] charge density with denser grid and wrong cube file

[Thomas Gruber]

Hallo all,

I have two problems:
1. I like to have the charge_density.xsf/*.cube with output_format=5/6, 
but with a denser grid than the FFT grid. nx,ny,nz are ignored in this 
case. They work for output_format=3 with an orthorhombic box, but I want 
my unit cell.

2. The output format for *.xsf works fine, but not for *.cube. For xsf 
the data_grid is x+1,y+1,z+1, but not for cube (x,y,z). The *.cube also 
needs x+1,y+1,z+1 to get the write volume, atom positions and no offset 
along the unit cell surface for the charge density. I tried to correct 
the cube.f90 in PP but the charge density data is still not correct. I 
increased nr# by 1 in each case:

   WRITE(ounit,*) 'Cubfile created from PWScf calculation'
   WRITE(ounit,*) ' Total SCF Density'
!origin is forced to (0.0,0.0,0.0)
   WRITE(ounit,'(I5,3F12.6)') nat, 0.0d0, 0.0d0, 0.0d0
   WRITE(ounit,'(I5,3F12.6)') nr1+1, (alat*at(i,1)/dble(nr1),i=1,3)
   WRITE(ounit,'(I5,3F12.6)') nr2+1, (alat*at(i,2)/dble(nr2),i=1,3)
   WRITE(ounit,'(I5,3F12.6)') nr3+1, (alat*at(i,3)/dble(nr3),i=1,3)

   DO i=1,nat
  nt = ityp(i)
  ! find atomic number for this atom.
  at_num = atomic_number(trim(atm(nt)))
  at_chrg= dble(at_num)
  ! at_chrg could be alternatively set to valence charge
  ! positions are in cartesian coordinates and a.u.
  !
  ! wrap coordinates back into cell.
  tpos = matmul( transpose(bg), tau(:,i) )
  tpos = tpos - nint(tpos - 0.5d0)
  inpos = alat * matmul( at, tpos )
  WRITE(ounit,'(I5,5F12.6)') at_num, at_chrg, inpos
   ENDDO

   DO i1=1,nr1+1
  DO i2=1,nr2+1
 WRITE(ounit,'(6E13.5)') (rho(i1,i2,i3),i3=1,nr3+1)
  ENDDO
   ENDDO

Can someone give me the correction for cube.f90 and a way to increase 
the data_grid density for the output_format=5/6?

Sincerely,

Thomas Gruber

-- 
Thomas Gruber
Institut f?r Theoretische Physik
TU Bergakademie Freiberg
Leipziger Str. 23, 09599 Freiberg, Germany
Tel: +49 (0)3731 392006
Email: thomas.gruber at physik.tu-freiberg.de

[Pw_forum] charge density difference

[Peng Chen]

Dear Dr. Giannozzi ,

Thank you very much for the reply. There are some differences between the
results from these 2 approaches. I prefer the approach with relaxed
structure since there are a lot of stress for the unrelaxed structure.

On Thu, Jan 17, 2013 at 6:56 AM, Paolo Giannozzi wrote:

> I don't think there is a "correct" way to perform
> the calculation you want, as opposed to an "incorrect"
> one. It depends what you want to show. Likely the difference
> between the two approaches will be invisible.
>
> P.
>
> On Tue, 2013-01-15 at 13:59 -0500, Peng Chen wrote:
> > Dear All,
> >
> >
> > I computed charge densities for two different spin states. There are
> > two ways:
> > 1) use experimental crystal structure without relaxation. The atomic
> > positions are exactly the same in two states.
> > 2) relax with fixed crystal dimensions (a, b, c). In this case, the
> > relaxed atomic positions are very close (difference <0.01\AA), but not
> > the same for two spin states.
> >
> >
> > The charge density difference for these two ways are different. I am
> > just curious which way will be  correct  to obtain the charge density
> > difference for two spin states?
> >
> >
> >
> > --
> >   Best Regards.
> > Peng
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
Peng
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[Pw_forum] charge density difference

[Paolo Giannozzi]

I don't think there is a "correct" way to perform
the calculation you want, as opposed to an "incorrect" 
one. It depends what you want to show. Likely the difference
between the two approaches will be invisible.

P.

On Tue, 2013-01-15 at 13:59 -0500, Peng Chen wrote:
> Dear All,
> 
> 
> I computed charge densities for two different spin states. There are
> two ways:
> 1) use experimental crystal structure without relaxation. The atomic
> positions are exactly the same in two states.
> 2) relax with fixed crystal dimensions (a, b, c). In this case, the
> relaxed atomic positions are very close (difference <0.01\AA), but not
> the same for two spin states. 
> 
> 
> The charge density difference for these two ways are different. I am
> just curious which way will be  correct  to obtain the charge density
> difference for two spin states?
> 
> 
> 
> -- 
>   Best Regards.
> Peng  
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

[Pw_forum] charge density difference

[Peng Chen]

Dear All,

I computed charge densities for two different spin states. There are two
ways:
1) use experimental crystal structure without relaxation. The atomic
positions are exactly the same in two states.
2) relax with fixed crystal dimensions (a, b, c). In this case, the relaxed
atomic positions are very close (difference <0.01\AA), but not the same for
two spin states.

The charge density difference for these two ways are different. I am just
curious which way will be  correct  to obtain the charge density difference
for two spin states?


-- 
  Best Regards.
Peng
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[Pw_forum] charge density units?

[Gisela Bocan]

There it is!
Thanks!!
Gisela.

On Tue, Oct 16, 2012 at 5:11 AM, Paolo Giannozzi wrote:

> On Mon, 2012-10-15 at 17:06 -0300, Gisela Bocan wrote:
>
> > I would need no know which units are used for the charge density.
> >  I've been googling on that for a while but no luck so far.
>
> it is explained in point 6.1 of the FAQs.
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] charge density units?

[Paolo Giannozzi]

On Mon, 2012-10-15 at 17:06 -0300, Gisela Bocan wrote:

> I would need no know which units are used for the charge density.
>  I've been googling on that for a while but no luck so far.

it is explained in point 6.1 of the FAQs.

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

[Pw_forum] charge density units?

[Gisela Bocan]

Hi,
 I am running pp.x for a Ag(110) surface. I choose iflag=2 and
output_format=2 in order to obtain a file that plotrho.x can read. I see in
the outfile that positions are given in alat units. I would need no know
which units are used for the charge density. I've been googling on that for
a while but no luck so far.
 Thanks in advance!
 Gisela.
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[Pw_forum] charge density difference calculation error!

[Yue-Wen Fang]

Dear Gabriele,

The attachment is the charge density given by pp.x. Left pic is no doping
and the right pic is N doped. These pictures present differently, so I
think the charge density shouldn't be zero.




2012/9/19 Gabriele Sclauzero 

>
> It seems to me that you have not completely understood how to use pp.x.
> If you take the difference between SRO-up.rho and SROup-doping.rho
> obtained with the inputs here below you will get zero, because they will
> contain the same charge density. You see why?
>
> GS
>
>
> Il giorno 19/set/2012, alle ore 10.15, Yue-Wen Fang ha scritto:
>
> The input files are listed here. In fact, there is no difference.
>
> 2012/9/19 Yue-Wen Fang 
>
>>
>> &inputpp
>> prefix = 'SRO'
>> outdir = './'
>> filplot = 'SROcharge'
>> plot_num= 0
>> spin_component=1
>> /
>> &plot
>> nfile = 1
>> filepp(1) = 'SROcharge'
>> weight(1) = 1.0
>> iflag = 2
>> output_format = 2
>> fileout = 'SRO-up.rho'
>> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
>> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
>> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
>> nx=56, ny=40
>> /
>>
>> &inputpp
>> prefix = 'SRO'
>> outdir = './'
>> filplot = 'SROcharge'
>> plot_num= 0
>> spin_component=1
>> /
>> &plot
>> nfile = 1
>> filepp(1) = 'SROcharge'
>> weight(1) = 1.0
>> iflag = 2
>> output_format = 2
>> fileout = 'SROup-doping.rho'
>> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
>> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
>> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
>> nx=56, ny=40
>> /
>>
>>
>> 2012/9/19 Gabriele Sclauzero 
>>
>>>
>>> I mean the header (the first 4 lines at least) of the density files that
>>> you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not
>>> the xsf files.
>>> Those lines contain information about the fft grid and are read by pp.x
>>> to check consistency between the grids in the two files.
>>>
>>> GS
>>>
>>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 

Yue-Wen Fang
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[Pw_forum] charge density difference calculation error!

[Yue-Wen Fang]

The input files are listed here. In fact, there is no difference.

2012/9/19 Yue-Wen Fang 

>
> &inputpp
> prefix = 'SRO'
> outdir = './'
> filplot = 'SROcharge'
> plot_num= 0
> spin_component=1
> /
> &plot
> nfile = 1
> filepp(1) = 'SROcharge'
> weight(1) = 1.0
> iflag = 2
> output_format = 2
> fileout = 'SRO-up.rho'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
> nx=56, ny=40
> /
>
> &inputpp
> prefix = 'SRO'
> outdir = './'
> filplot = 'SROcharge'
> plot_num= 0
> spin_component=1
> /
> &plot
> nfile = 1
> filepp(1) = 'SROcharge'
> weight(1) = 1.0
> iflag = 2
> output_format = 2
> fileout = 'SROup-doping.rho'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
> nx=56, ny=40
> /
>
>
> 2012/9/19 Gabriele Sclauzero 
>
>>
>> I mean the header (the first 4 lines at least) of the density files that
>> you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not
>> the xsf files.
>> Those lines contain information about the fft grid and are read by pp.x
>> to check consistency between the grids in the two files.
>>
>> GS
>>
>> Il giorno 18/set/2012, alle ore 17.09, Yue-Wen Fang ha scritto:
>>
>> Do you mean the output file?
>> the header of output file in xsf* with Nitrogen doping*:
>>  CRYSTAL
>>  PRIMVEC
>> 3.9050012970.00.0
>> 0.03.9050012970.0
>> 0.00.03.905001297
>>  PRIMCOORD
>>5   1
>> Sr0.00.00.0
>> Ru1.9525006491.9525006491.952500649
>> O 1.9525006490.01.952500649
>> O 0.01.9525006491.952500649
>> O 1.9525006491.9525006490.0
>> 
>> 
>>
>> the header of output file in xsf* without Nitrogen doping*:
>>  CRYSTAL
>>  PRIMVEC
>> 3.9050012970.00.0
>> 0.03.9050012970.0
>> 0.00.03.905001297
>>  PRIMCOORD
>>5   1
>> Sr0.00.00.0
>> Ru1.9525006491.9525006491.952500649
>> O 1.9525006490.01.952500649
>> O 0.01.9525006491.952500649
>> O 1.9525006491.9525006490.0
>>
>> The two headers are same.
>> Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory
>> building and go to sleep.
>> Thank you for your help.
>>
>> Best wishes!
>> Yuewen Fang
>>
>> 2012/9/18 Gabriele Sclauzero 
>>
>>> Could you please provide the header of the two density files?
>>>
>>> Thanks,
>>>
>>> GS
>>>
>>>
>>> Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto:
>>>
>>> The cells are same size and the cutoff is also same. The difference is
>>> that in the second cell I used a pseudopotential generated by virtual.x
>>> (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual
>>> crystal approximation method to simulate the SRO system doped by nitrogen.
>>>
>>> Best wishes!
>>>
>>>
>>>
>>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>>> *   PH H2 462, Station 3, CH-1015 Lausanne*
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>> --
>> 
>> Yue-Wen Fang
>>
>>
>>
>>  ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>
>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>> *   PH H2 462, Station 3, CH-1015 Lausanne*
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> 
> Yue-Wen Fang
>
>
>
>


-- 

Yue-Wen Fang
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[Pw_forum] charge density difference calculation error!

[Yue-Wen Fang]

&inputpp
prefix = 'SRO'
outdir = './'
filplot = 'SROcharge'
plot_num= 0
spin_component=1
/
&plot
nfile = 1
filepp(1) = 'SROcharge'
weight(1) = 1.0
iflag = 2
output_format = 2
fileout = 'SRO-up.rho'
e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
nx=56, ny=40
/

&inputpp
prefix = 'SRO'
outdir = './'
filplot = 'SROcharge'
plot_num= 0
spin_component=1
/
&plot
nfile = 1
filepp(1) = 'SROcharge'
weight(1) = 1.0
iflag = 2
output_format = 2
fileout = 'SROup-doping.rho'
e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
nx=56, ny=40
/


2012/9/19 Gabriele Sclauzero 

>
> I mean the header (the first 4 lines at least) of the density files that
> you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not
> the xsf files.
> Those lines contain information about the fft grid and are read by pp.x to
> check consistency between the grids in the two files.
>
> GS
>
> Il giorno 18/set/2012, alle ore 17.09, Yue-Wen Fang ha scritto:
>
> Do you mean the output file?
> the header of output file in xsf* with Nitrogen doping*:
>  CRYSTAL
>  PRIMVEC
> 3.9050012970.00.0
> 0.03.9050012970.0
> 0.00.03.905001297
>  PRIMCOORD
>5   1
> Sr0.00.00.0
> Ru1.9525006491.9525006491.952500649
> O 1.9525006490.01.952500649
> O 0.01.9525006491.952500649
> O 1.9525006491.9525006490.0
> 
> 
>
> the header of output file in xsf* without Nitrogen doping*:
>  CRYSTAL
>  PRIMVEC
> 3.9050012970.00.0
> 0.03.9050012970.0
> 0.00.03.905001297
>  PRIMCOORD
>5   1
> Sr0.00.00.0
> Ru1.9525006491.9525006491.952500649
> O 1.9525006490.01.952500649
> O 0.01.9525006491.952500649
> O 1.9525006491.9525006490.0
>
> The two headers are same.
> Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory
> building and go to sleep.
> Thank you for your help.
>
> Best wishes!
> Yuewen Fang
>
> 2012/9/18 Gabriele Sclauzero 
>
>> Could you please provide the header of the two density files?
>>
>> Thanks,
>>
>> GS
>>
>>
>> Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto:
>>
>> The cells are same size and the cutoff is also same. The difference is
>> that in the second cell I used a pseudopotential generated by virtual.x
>> (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual
>> crystal approximation method to simulate the SRO system doped by nitrogen.
>>
>> Best wishes!
>>
>>
>>
>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>> *   PH H2 462, Station 3, CH-1015 Lausanne*
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> 
> Yue-Wen Fang
>
>
>
>  ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
>
>
>
>
>
>
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> http://www.democritos.it/mailman/listinfo/pw_forum
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>


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[Pw_forum] charge density difference calculation error!

[Gabriele Sclauzero]

Moreover, this is not the way to proceed. The files read in chdens.f90 
(filepp(*) in the &plot section) are those listed in the &inputpp section 
(filplot). 
They can be produced in the same run of pp.x or in a previous run(s).
If you need charge differences you need to run twice pp.x specifying only the 
&inputpp section, and then once more using only the &plot section.

HTH


GS

Il giorno 19/set/2012, alle ore 10.37, Gabriele Sclauzero ha scritto:

> 
> It seems to me that you have not completely understood how to use pp.x.
> If you take the difference between SRO-up.rho and SROup-doping.rho obtained 
> with the inputs here below you will get zero, because they will contain the 
> same charge density. You see why?
> 
> GS
> 
> 
> Il giorno 19/set/2012, alle ore 10.15, Yue-Wen Fang ha scritto:
> 
>> The input files are listed here. In fact, there is no difference.
>> 
>> 2012/9/19 Yue-Wen Fang 
>> 
>> &inputpp
>> prefix = 'SRO'
>> outdir = './'
>> filplot = 'SROcharge'
>> plot_num= 0
>> spin_component=1
>> /
>> &plot
>> nfile = 1
>> filepp(1) = 'SROcharge'
>> weight(1) = 1.0
>> iflag = 2
>> output_format = 2
>> fileout = 'SRO-up.rho'
>> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
>> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
>> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
>> nx=56, ny=40
>> /
>> 
>> &inputpp
>> prefix = 'SRO'
>> outdir = './'
>> filplot = 'SROcharge'
>> plot_num= 0
>> spin_component=1
>> /
>> &plot
>> nfile = 1
>> filepp(1) = 'SROcharge'
>> weight(1) = 1.0
>> iflag = 2
>> output_format = 2
>> fileout = 'SROup-doping.rho'
>> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
>> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
>> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
>> nx=56, ny=40
>> /
>> 
>> 
>> 2012/9/19 Gabriele Sclauzero 
>> 
>> I mean the header (the first 4 lines at least) of the density files that you 
>> are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not the 
>> xsf files.
>> Those lines contain information about the fft grid and are read by pp.x to 
>> check consistency between the grids in the two files.
>> 
>> GS 
> 
> 
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>PH H2 462, Station 3, CH-1015 Lausanne
> 
> 
> 
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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   PH H2 462, Station 3, CH-1015 Lausanne







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[Pw_forum] charge density difference calculation error!

[Gabriele Sclauzero]

It seems to me that you have not completely understood how to use pp.x.
If you take the difference between SRO-up.rho and SROup-doping.rho obtained 
with the inputs here below you will get zero, because they will contain the 
same charge density. You see why?

GS


Il giorno 19/set/2012, alle ore 10.15, Yue-Wen Fang ha scritto:

> The input files are listed here. In fact, there is no difference.
> 
> 2012/9/19 Yue-Wen Fang 
> 
> &inputpp
> prefix = 'SRO'
> outdir = './'
> filplot = 'SROcharge'
> plot_num= 0
> spin_component=1
> /
> &plot
> nfile = 1
> filepp(1) = 'SROcharge'
> weight(1) = 1.0
> iflag = 2
> output_format = 2
> fileout = 'SRO-up.rho'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
> nx=56, ny=40
> /
> 
> &inputpp
> prefix = 'SRO'
> outdir = './'
> filplot = 'SROcharge'
> plot_num= 0
> spin_component=1
> /
> &plot
> nfile = 1
> filepp(1) = 'SROcharge'
> weight(1) = 1.0
> iflag = 2
> output_format = 2
> fileout = 'SROup-doping.rho'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
> nx=56, ny=40
> /
> 
> 
> 2012/9/19 Gabriele Sclauzero 
> 
> I mean the header (the first 4 lines at least) of the density files that you 
> are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not the 
> xsf files.
> Those lines contain information about the fft grid and are read by pp.x to 
> check consistency between the grids in the two files.
> 
> GS 


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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[Pw_forum] charge density difference calculation error!

[Gabriele Sclauzero]

I mean the header (the first 4 lines at least) of the density files that you 
are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not the xsf 
files.
Those lines contain information about the fft grid and are read by pp.x to 
check consistency between the grids in the two files.

GS 

Il giorno 18/set/2012, alle ore 17.09, Yue-Wen Fang ha scritto:

> Do you mean the output file?
> the header of output file in xsf with Nitrogen doping:
>  CRYSTAL
>  PRIMVEC
> 3.9050012970.00.0
> 0.03.9050012970.0
> 0.00.03.905001297
>  PRIMCOORD
>5   1
> Sr0.00.00.0
> Ru1.9525006491.9525006491.952500649
> O 1.9525006490.01.952500649
> O 0.01.9525006491.952500649
> O 1.9525006491.9525006490.0
> 
> 
> 
> the header of output file in xsf without Nitrogen doping:
>  CRYSTAL
>  PRIMVEC
> 3.9050012970.00.0
> 0.03.9050012970.0
> 0.00.03.905001297
>  PRIMCOORD
>5   1
> Sr0.00.00.0
> Ru1.9525006491.9525006491.952500649
> O 1.9525006490.01.952500649
> O 0.01.9525006491.952500649
> O 1.9525006491.9525006490.0
> 
> The two headers are same.
> Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory 
> building and go to sleep.
> Thank you for your help.
> 
> Best wishes!
> Yuewen Fang
> 
> 2012/9/18 Gabriele Sclauzero 
> Could you please provide the header of the two density files?
> 
> Thanks,
> 
> GS
> 
> 
> Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto:
> 
>> The cells are same size and the cutoff is also same. The difference is that 
>> in the second cell I used a pseudopotential generated by virtual.x (the pp 
>> mix N.*.UPF and O.*.UPF), in the other words, i used the virtual crystal 
>> approximation method to simulate the SRO system doped by nitrogen.
>> 
>> Best wishes!
> 
> 
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>PH H2 462, Station 3, CH-1015 Lausanne
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> 
> -- 
> 
> Yue-Wen Fang
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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[Pw_forum] charge density difference calculation error!

[Yue-Wen Fang]

Do you mean the output file?
the header of output file in xsf* with Nitrogen doping*:
 CRYSTAL
 PRIMVEC
3.9050012970.00.0
0.03.9050012970.0
0.00.03.905001297
 PRIMCOORD
   5   1
Sr0.00.00.0
Ru1.9525006491.9525006491.952500649
O 1.9525006490.01.952500649
O 0.01.9525006491.952500649
O 1.9525006491.9525006490.0



the header of output file in xsf* without Nitrogen doping*:
 CRYSTAL
 PRIMVEC
3.9050012970.00.0
0.03.9050012970.0
0.00.03.905001297
 PRIMCOORD
   5   1
Sr0.00.00.0
Ru1.9525006491.9525006491.952500649
O 1.9525006490.01.952500649
O 0.01.9525006491.952500649
O 1.9525006491.9525006490.0

The two headers are same.
Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory
building and go to sleep.
Thank you for your help.

Best wishes!
Yuewen Fang

2012/9/18 Gabriele Sclauzero 

> Could you please provide the header of the two density files?
>
> Thanks,
>
> GS
>
>
> Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto:
>
> The cells are same size and the cutoff is also same. The difference is
> that in the second cell I used a pseudopotential generated by virtual.x
> (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual
> crystal approximation method to simulate the SRO system doped by nitrogen.
>
> Best wishes!
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


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[Pw_forum] charge density difference calculation error!

[Yue-Wen Fang]

The cells are same size and the cutoff is also same. The difference is that
in the second cell I used a pseudopotential generated by virtual.x (the pp
mix N.*.UPF and O.*.UPF), in the other words, i used the virtual crystal
approximation method to simulate the SRO system doped by nitrogen.

Best wishes!

2012/9/18 Gabriele Sclauzero 

>
> Il giorno 18/set/2012, alle ore 14.55, Yue-Wen Fang ha scritto:
>
> Dear all,
> It happened a problem to me when calculating the charge density
> difference.
> *My input*:
> &inputpp
> /
> &plot
> nfile = 2
> filepp(1) = 'SRO-up.rho'   *(SRO-up.rho is a file which records the
> charge density data of this system, it was given at last step)*
> filepp(2) = 'SROup-doping.rho'
> weight(1) = 1.0
> weight(2) = -1.0
> iflag = 2
> output_format = 3
> fileout = 'test_diff.xsf'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
> nx=56, ny=40
> /
> *The output*:
>  R & G space division:  proc/pool =4
>  Reading header from file  SRO-up.rho
>  Reading data from file  SRO-up.rho
>
>
>  
> %%
>  from chdens : error # 1
>  *incompatible nr1x or nr2x(I haven't found what nr1x means)*
>
>  
> %%
>
>  stopping ...
>
>
> Most probably there is a size mismatch between the two cells, or you used
> a different cutoff for the two calculations. Please check.
>
>
> GS
>
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


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[Pw_forum] charge density difference calculation error!

[Yue-Wen Fang]

Dear all,
It happened a problem to me when calculating the charge density difference.
*My input*:
&inputpp
/
&plot
nfile = 2
filepp(1) = 'SRO-up.rho'   *(SRO-up.rho is a file which records the
charge density data of this system, it was given at last step)*
filepp(2) = 'SROup-doping.rho'
weight(1) = 1.0
weight(2) = -1.0
iflag = 2
output_format = 3
fileout = 'test_diff.xsf'
e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
nx=56, ny=40
/
*The output*:
 R & G space division:  proc/pool =4
 Reading header from file  SRO-up.rho
 Reading data from file  SRO-up.rho

 %%
 from chdens : error # 1
 *incompatible nr1x or nr2x(I haven't found what nr1x means)*
 %%

 stopping ...

 %%
 from chdens : error # 1
 incompatible nr1x or nr2x
 %%

 stopping ...

 %%
 from chdens : error # 1
 incompatible nr1x or nr2x
 %%

 stopping ...

 %%
 from chdens : error # 1
 incompatible nr1x or nr2x
 %%

 stopping ...
p0_22690:  p4_error: : 0
rm_l_1_22720: (0.140625) net_send: could not write to fd=5, errno = 32
rm_l_3_22778: (0.058594) net_send: could not write to fd=5, errno = 32
p0_22690: (4.222656) net_send: could not write to fd=4, errno = 32
p1_22695: (4.144531) net_send: could not write to fd=5, errno = 32
p3_22753: (4.062500) net_send: could not write to fd=5, errno = 32


-- 

Yue-Wen Fang
Shanghai, China
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[Pw_forum] charge density difference calculation error!

[Gabriele Sclauzero]

Could you please provide the header of the two density files?

Thanks,

GS


Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto:

> The cells are same size and the cutoff is also same. The difference is that 
> in the second cell I used a pseudopotential generated by virtual.x (the pp 
> mix N.*.UPF and O.*.UPF), in the other words, i used the virtual crystal 
> approximation method to simulate the SRO system doped by nitrogen.
> 
> Best wishes!


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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[Pw_forum] charge density difference calculation error!

[Gabriele Sclauzero]

Il giorno 18/set/2012, alle ore 14.55, Yue-Wen Fang ha scritto:

> Dear all,
> It happened a problem to me when calculating the charge density difference. 
> My input:
> &inputpp
> /
> &plot
> nfile = 2
> filepp(1) = 'SRO-up.rho'   (SRO-up.rho is a file which records the charge 
> density data of this system, it was given at last step)
> filepp(2) = 'SROup-doping.rho'
> weight(1) = 1.0
> weight(2) = -1.0
> iflag = 2
> output_format = 3
> fileout = 'test_diff.xsf'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0,
> nx=56, ny=40
> /
> The output:
>  R & G space division:  proc/pool =4
>  Reading header from file  SRO-up.rho
>  Reading data from file  SRO-up.rho
> 
>  
> %%
>  from chdens : error # 1
>  incompatible nr1x or nr2x(I haven't found what nr1x means)
>  
> %%
> 
>  stopping ...

Most probably there is a size mismatch between the two cells, or you used a 
different cutoff for the two calculations. Please check.


GS




? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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[Pw_forum] Charge Density of the Graphene-Lithium System

[Thaneshwor Kaloni]

Dear Gulcin,

Please run three scf in three different out directory like as,
1) graphene+Li
2)graphene
3)Li

Then run three post processing by pp.x
1) graphene+Li
2)graphene
3)Li

Then, run a final post processing by pp.x
The final input looking  like one pasted below,

 &inputpp
/
&plot
nfile=3
filepp(1)='all.charge'
filepp(2)='Li.charge'
filepp(3)='graphene.charge'
weight(1)=1
weight(2)=-1
weight(3)=-1
iflag=3
output_format=5
fileout='chden.xsf'
/

Finally, plot chden.xsf file.
I hope it will help you.

Kaloni

KAUST, KSA



Message: 6
Date: Fri, 6 Jul 2012 12:42:23 -0400
From: Gulcin Kucukdalyan 
Subject: [Pw_forum] Charge Density of the Graphene-Lithium System
To: PWSCF Forum 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi All,

I am trying to calculate the charge density of the graphene -lithium system
by showing the negative and positive regions on it. When i uploaded the
below input file to Xcrysden i cannnot see  either  the negative and
positive regions  nor  the charge flow on 3D Xccrysden figure. How should i
modify my file to do so?

Thansk in advance,

Gulcin

# self-consistent calculation
cat > gli.scf.in << EOF
 &control
calculation = 'scf'
restart_mode='from_scratch',
prefix='gli',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
 /
 &system
ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
ecutwfc =60.0,
ecutrho = 500.0
 occupations='smearing', smearing='methfessel-paxton', degauss=0.02
 /
 &electrons
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr =  1.0d-7
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-rrkjus.UPF
 Li  6.9142   Li.pz-n-vbc.UPF
ATOMIC_POSITIONS
C   -0.000169177  -0.000292351   0.0
C0.333413183  -0.000292351   0.0
C0.500204479   0.288597992   0.0
C0.333413183   0.577488334   0.0
C   -0.000169177   0.577488334   0.0
C   -0.166960373   0.288597992   0.0
Li   0.166621953   0.288597992   0.416524683
K_POINTS AUTOMATIC
5 5 6 0 0 0
EOF
$ECHO "  running the scf calculation for Gr-Li...\c"
$PW_COMMAND < gli.scf.in > gli.scf.out
check_failure $?
$ECHO " done"

# post-processing for charge density
cat > gli.pp.in << EOF
   &inputpp
   prefix  = 'gli'
   outdir = '$TMP_DIR/'
   filplot = 'gli.pp'
   plot_num= 7
   kpoint = 1
   kband = 14
   spin_component = 0

/

 &plot
nfile = 1
filepp(1) = 'gli.pp'
weight(1) = 1.0
iflag = 3
output_format = 5
fileout = 'gli.xsf'
/
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[Pw_forum] Charge Density of the Graphene-Lithium System

[Gulcin Kucukdalyan]

Hi All,

I am trying to calculate the charge density of the graphene -lithium system
by showing the negative and positive regions on it. When i uploaded the
below input file to Xcrysden i cannnot see  either  the negative and
positive regions  nor  the charge flow on 3D Xccrysden figure. How should i
modify my file to do so?

Thansk in advance,

Gulcin

# self-consistent calculation
cat > gli.scf.in << EOF
 &control
calculation = 'scf'
restart_mode='from_scratch',
prefix='gli',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
 /
 &system
ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
ecutwfc =60.0,
ecutrho = 500.0
 occupations='smearing', smearing='methfessel-paxton', degauss=0.02
 /
 &electrons
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr =  1.0d-7
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-rrkjus.UPF
 Li  6.9142   Li.pz-n-vbc.UPF
ATOMIC_POSITIONS
C   -0.000169177  -0.000292351   0.0
C0.333413183  -0.000292351   0.0
C0.500204479   0.288597992   0.0
C0.333413183   0.577488334   0.0
C   -0.000169177   0.577488334   0.0
C   -0.166960373   0.288597992   0.0
Li   0.166621953   0.288597992   0.416524683
K_POINTS AUTOMATIC
5 5 6 0 0 0
EOF
$ECHO "  running the scf calculation for Gr-Li...\c"
$PW_COMMAND < gli.scf.in > gli.scf.out
check_failure $?
$ECHO " done"

# post-processing for charge density
cat > gli.pp.in << EOF
   &inputpp
   prefix  = 'gli'
   outdir = '$TMP_DIR/'
   filplot = 'gli.pp'
   plot_num= 7
   kpoint = 1
   kband = 14
   spin_component = 0

/

 &plot
nfile = 1
filepp(1) = 'gli.pp'
weight(1) = 1.0
iflag = 3
output_format = 5
fileout = 'gli.xsf'
/
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[Pw_forum] Charge density as a percentage

[Stefano de Gironcoli]

a post-processing tool that can be used for that purpose is the 
projwfc.x code (check for it in the PP subdirectory) which calculates 
the  density of state projected on the atomic orbitals.
consider however that any decomposition of density in atomic 
contributions is somehow arbitrary and
you should not believe too much in the precise numbers you obtain

stefano

On 07/01/2012 07:08 PM, Gulcin Tetiker wrote:
> Hi All,
>
> I was just wondering if it is possible to calculate the charge percentage of 
> li- graphene system. What i mean is that being able to calculate the charge 
> percentage of lithium and graphene separately in the whole lithium-graphene 
> system.
>
> Regards,
>
> Gulcin
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

[Pw_forum] Charge density as a percentage

[Gulcin Tetiker]

Hi All, 

I was just wondering if it is possible to calculate the charge percentage of 
li- graphene system. What i mean is that being able to calculate the charge 
percentage of lithium and graphene separately in the whole lithium-graphene 
system. 

Regards,

Gulcin

[Pw_forum] Charge Density of Each State

[Layla Martin-Samos]

If you want to print the LUMO, you need firts in the pw.x input ask for
calculating more bands,

supose you have SiH4 molecule, 8 electrons --> 4 occupied bands, lumo has
band index 5

you need to make pw.x calculation with nband = 5 (in system namelist)

then for pp.x calculation kband=5

and so you will get the LUMO

But realy, first read a text book on solid state physics.

best regards

Layla

2012/6/28 Gulcin Tetiker 

> Thanks a lot for the info. I got the idea. So does it mean that if i want
> to calculate LUMO do i have to add 1 to the HOMO so that the code can print
> the LUMO level?
>
> On Jun 28, 2012, at 11:38 AM, Layla Martin-Samos 
> wrote:
>
> Dear Gulcin, first you need to know of many electrons you have. Carbon,
> with only valence electrons means 4 electrons for each carbon (you have
> this information in the pseudopotential file). Then you have to count two
> electrons (spin up spin down) per band. If your system has 25 electrons
> then you have 12 bands with two electrons and one band with only 1
> electron. You should read a text book on solid state physics such as
> Ashcroft and Mermin.
>
> For input pp.x, if you write kband = 10 , print in xsf format the
> "orbital" corresponding to this band. Supose you have a molecule like SiH4
> -> 8 electrons -> 4 occupied bands. If you run pw.x wihtout nband = 
> Then the code computes the energy and wave-functions only for the occupied
> bands (the 4 occupied bands). Then if you wirte in pp.x input kband=4 it
> will print the "orbital" called HOMO --> the "last" occupied
> wavefunction/electronic state.
>
> best regards
>
> Layla
>
> 2012/6/28 Gulcin Tetiker 
>
>> Thank you. It solve the problem. Could you please tell me how did you get
>> 17?
>>
>> Sent from my iPhone
>>
>> On Jun 28, 2012, at 10:53 AM, giannozz at democritos.it wrote:
>>
>> > Quoting Gulcin Tetiker :
>> >
>> >> Thanks Duy. I changed it to 25 but it still gives error.
>> >
>> > of course it does: your input produces 17 bands
>> >
>> > Paolo
>> >
>> >
>> > 
>> > This message was sent using IMP, the Internet Messaging Program.
>> >
>> > ___
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> ___
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> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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[Pw_forum] Charge Density of Each State

[Thaneshwor Kaloni]

Dear Gulcin Kucukdalyan,

Recently, I have reported this system (C6Li) and I did not encountered any
problem.
I think it would be helpful if you look at the following paper
http://www.sciencedirect.com/science/article/pii/S0009261412003004

Best, kaloni
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[Pw_forum] Charge Density of Each State

[Lorenzo Paulatto]

On Thu, Jun 28, 2012 at 6:02 PM, Gulcin Tetiker wrote:

> Thanks a lot for the info. I got the idea. So does it mean that if i want
> to calculate LUMO do i have to add 1 to the HOMO so that the code can print
> the LUMO level?
>


The code normally does not compute the LUMO; you need to manually set the
number of bands (nbnd) to get it.

bests

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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[Pw_forum] Charge Density of Each State

[Layla Martin-Samos]

Dear Gulcin, first you need to know of many electrons you have. Carbon,
with only valence electrons means 4 electrons for each carbon (you have
this information in the pseudopotential file). Then you have to count two
electrons (spin up spin down) per band. If your system has 25 electrons
then you have 12 bands with two electrons and one band with only 1
electron. You should read a text book on solid state physics such as
Ashcroft and Mermin.

For input pp.x, if you write kband = 10 , print in xsf format the "orbital"
corresponding to this band. Supose you have a molecule like SiH4 -> 8
electrons -> 4 occupied bands. If you run pw.x wihtout nband =  Then
the code computes the energy and wave-functions only for the occupied bands
(the 4 occupied bands). Then if you wirte in pp.x input kband=4 it will
print the "orbital" called HOMO --> the "last" occupied
wavefunction/electronic state.

best regards

Layla

2012/6/28 Gulcin Tetiker 

> Thank you. It solve the problem. Could you please tell me how did you get
> 17?
>
> Sent from my iPhone
>
> On Jun 28, 2012, at 10:53 AM, giannozz at democritos.it wrote:
>
> > Quoting Gulcin Tetiker :
> >
> >> Thanks Duy. I changed it to 25 but it still gives error.
> >
> > of course it does: your input produces 17 bands
> >
> > Paolo
> >
> >
> > 
> > This message was sent using IMP, the Internet Messaging Program.
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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[Pw_forum] Charge Density of Each State

[giann...@democritos.it]

Quoting Gulcin Tetiker :

> Thanks Duy. I changed it to 25 but it still gives error.

of course it does: your input produces 17 bands

Paolo



This message was sent using IMP, the Internet Messaging Program.

[Pw_forum] Charge Density of Each State

[Gulcin Tetiker]

As far as i understand whatever kband number i write as an input QE print the 
output of that file. So my question is that if i want to calculate all bands do 
i need to write them all by separating them with space, comma etc.

How about for kpoint? Does it just calculate the kpoint specifies by the code? 
For example kpoint= 1 just do calculation for only the first kpoint. How about 
if i wanna calculate for all k points?
 Thanks

On Jun 28, 2012, at 12:11 PM, Lorenzo Paulatto  wrote:

> On Thu, Jun 28, 2012 at 6:02 PM, Gulcin Tetiker  
> wrote:
> Thanks a lot for the info. I got the idea. So does it mean that if i want to 
> calculate LUMO do i have to add 1 to the HOMO so that the code can print the 
> LUMO level?
> 
> 
> The code normally does not compute the LUMO; you need to manually set the 
> number of bands (nbnd) to get it.
> 
> bests
> 
> -- 
> Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] Charge Density of Each State

[Gulcin Tetiker]

Should i do separate calculations like nbnd= 12 and later 13, etc. or can i 
write all down by separating with spaces, comma, etc.

 Gulcin

On Jun 28, 2012, at 12:11 PM, Lorenzo Paulatto  wrote:

> On Thu, Jun 28, 2012 at 6:02 PM, Gulcin Tetiker  
> wrote:
> Thanks a lot for the info. I got the idea. So does it mean that if i want to 
> calculate LUMO do i have to add 1 to the HOMO so that the code can print the 
> LUMO level?
> 
> 
> The code normally does not compute the LUMO; you need to manually set the 
> number of bands (nbnd) to get it.
> 
> bests
> 
> -- 
> Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] Charge Density of Each State

[Gulcin Tetiker]

Thanks a lot for the info. I got the idea. So does it mean that if i want to 
calculate LUMO do i have to add 1 to the HOMO so that the code can print the 
LUMO level?

On Jun 28, 2012, at 11:38 AM, Layla Martin-Samos  
wrote:

> Dear Gulcin, first you need to know of many electrons you have. Carbon, with 
> only valence electrons means 4 electrons for each carbon (you have this 
> information in the pseudopotential file). Then you have to count two 
> electrons (spin up spin down) per band. If your system has 25 electrons then 
> you have 12 bands with two electrons and one band with only 1 electron. You 
> should read a text book on solid state physics such as Ashcroft and Mermin. 
> 
> For input pp.x, if you write kband = 10 , print in xsf format the "orbital" 
> corresponding to this band. Supose you have a molecule like SiH4 -> 8 
> electrons -> 4 occupied bands. If you run pw.x wihtout nband =  Then the 
> code computes the energy and wave-functions only for the occupied bands (the 
> 4 occupied bands). Then if you wirte in pp.x input kband=4 it will print the 
> "orbital" called HOMO --> the "last" occupied wavefunction/electronic state.
> 
> best regards
> 
> Layla
> 
> 2012/6/28 Gulcin Tetiker 
> Thank you. It solve the problem. Could you please tell me how did you get 17?
> 
> Sent from my iPhone
> 
> On Jun 28, 2012, at 10:53 AM, giannozz at democritos.it wrote:
> 
> > Quoting Gulcin Tetiker :
> >
> >> Thanks Duy. I changed it to 25 but it still gives error.
> >
> > of course it does: your input produces 17 bands
> >
> > Paolo
> >
> >
> > 
> > This message was sent using IMP, the Internet Messaging Program.
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> ___
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> Pw_forum at pwscf.org
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[Pw_forum] Charge Density of Each State

[Guido Fratesi]

BTW, your cutoffs are larger than what I would have expected. Are you 
sure you really need them to converge your calculations?
Guido

On 06/28/2012 12:19 AM, Gulcin Kucukdalyan wrote:
> Below is my input and output file:
>
> INpiut:
>
>   # self-consistent calculation
>  cat > gli.scf.in  << EOF
>   &control
>  calculation = 'scf'
>  restart_mode='from_scratch',
>  prefix='gli',
>  pseudo_dir = '$PSEUDO_DIR/',
>  outdir='$TMP_DIR/'
>   /
>   &system
>  ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
>  ecutwfc =60.0,
>  ecutrho = 500.0
>   occupations='smearing', smearing='methfessel-paxton', degauss=0.02
>   /
>   &electrons
>  mixing_mode = 'plain'
>  mixing_beta = 0.7
>  conv_thr =  1.0d-7
>   /
> ATOMIC_SPECIES
>   C   12.0107  C.pz-rrkjus.UPF
>   Li  6.9142   Li.pz-n-vbc.UPF
> ATOMIC_POSITIONS
> C   -0.000169177  -0.000292351   0.0
> C0.333413183  -0.000292351   0.0
> C0.500204479   0.288597992   0.0
> C0.333413183   0.577488334   0.0
> C   -0.000169177   0.577488334   0.0
> C   -0.166960373   0.288597992   0.0
> Li   0.166621953   0.288597992   0.416524683
> K_POINTS AUTOMATIC
> 5 5 6 0 0 0
> EOF

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

[Pw_forum] Charge Density of Each State

[Gulcin Tetiker]

Thank you. It solve the problem. Could you please tell me how did you get 17? 

Sent from my iPhone

On Jun 28, 2012, at 10:53 AM, giannozz at democritos.it wrote:

> Quoting Gulcin Tetiker :
> 
>> Thanks Duy. I changed it to 25 but it still gives error.
> 
> of course it does: your input produces 17 bands
> 
> Paolo
> 
> 
> 
> This message was sent using IMP, the Internet Messaging Program.
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
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[Pw_forum] Charge Density of Each State

[Gulcin Tetiker]

Thanks Duy. I changed it to 25 but it still gives error. 

On Jun 27, 2012, at 6:27 PM, Duy Le  wrote:

> You should check out how many bands you have in your calculations. It looks 
> like to me that you don't have that many bands.
> 6 C + 1 Li -> 25 electrons
> 
> Duy Le
> Postdoctoral Associate
> Department of Physics
> University of Central Florida.
> Website: http://www.physics.ucf.edu/~dle
> 
> 
> On Wed, Jun 27, 2012 at 6:19 PM, Gulcin Kucukdalyan  gmail.com> wrote:
> Below is my input and output file:
> 
> INpiut:
> 
>  # self-consistent calculation
> cat > gli.scf.in << EOF
>  &control
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='gli',
> pseudo_dir = '$PSEUDO_DIR/',
> outdir='$TMP_DIR/'
>  /
>  &system
> ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
> ecutwfc =60.0,
> ecutrho = 500.0
>  occupations='smearing', smearing='methfessel-paxton', degauss=0.02
>  /
>  &electrons
> mixing_mode = 'plain'
> mixing_beta = 0.7
> conv_thr =  1.0d-7
>  /
> ATOMIC_SPECIES
>  C   12.0107  C.pz-rrkjus.UPF
>  Li  6.9142   Li.pz-n-vbc.UPF
> ATOMIC_POSITIONS
> C   -0.000169177  -0.000292351   0.0
> C0.333413183  -0.000292351   0.0
> C0.500204479   0.288597992   0.0
> C0.333413183   0.577488334   0.0
> C   -0.000169177   0.577488334   0.0
> C   -0.166960373   0.288597992   0.0
> Li   0.166621953   0.288597992   0.416524683
> K_POINTS AUTOMATIC
> 5 5 6 0 0 0 
> EOF
> $ECHO "  running the scf calculation for Gr-Li...\c"
> $PW_COMMAND < gli.scf.in > gli.scf.out
> check_failure $?
> $ECHO " done"
> 
> # post-processing for charge density
> cat > gli.pp.in << EOF
>&inputpp
>prefix  = 'gli'
>outdir = '$TMP_DIR/'
>filplot = 'gli.pp'
>plot_num= 7
>kpoint = 36
>kband = 32
>spin_component = 0
>
> /
> 
>  &plot
> nfile = 1
> filepp(1) = 'gli.pp'
> weight(1) = 1.0
> iflag = 3
> output_format = 5
> fileout = 'gli.xsf'
> /
> 
> 
> Output:
> 
>   Plotting k_point =  36  band = 32
> 
>  
> %%
> 
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>  
> %%
> 
>  stopping ...
> 
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>  
> %%
> 
>  stopping ...
> 
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>  
> %%
> 
>  stopping ...
>  from local_dos : error # 1
>  wrong band specified
>  
> %%
> 
>  stopping ...
> 
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>  
> %%
> 
>  stopping ...
> 
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>  
> %%
> 
>  stopping ...
> 
> Thank you
> 
> 
> 
> On Wed, Jun 27, 2012 at 5:31 PM, Lorenzo Paulatto  impmc.upmc.fr> wrote:
> On Wed, Jun 27, 2012 at 11:03 PM, Gulcin Tetiker  
> wrote:
> Thanks for the response. I used those numbers also but the code gave error. I 
> guess they symbolize different things. For example, if we only wanna 
> calculate the charge density in gamma point kpoint should be 1. Also, for 
> kband someone use "band near fermi level". I was just wondering where can i 
> get all these information
> 
> I do not understand what you mean by "band near fermi level". 
> 
> kband is an interger positive number, it must be smaller or equal to the 
> number of bands.
> 
> If you are getting some erro, please report which error you get, maybe it has 
> nothing to do with the value of kband. A good idea is to alway provide a copy 
> of your input and out when you have a problem.
> 
> bests
> 
> 
> -- 
> Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
> 
> 
> ___
> Pw_forum mailing lis