[Pw_forum] QUERY RELATED TO THE FERMI ENERGY?

[Dhara Raval]

Dear forum,


THANKS FOR YOUR VALUABLE TIME FOR MY QUERY...

I have face one query related to the Fermi energy...when i run the program
for band structure then SCF file generated and in this output file  Fermi
energy is 10.9937 eV... then after i run the Fermi surfaces program again
the SCF output Dat file generated also...in this SCF file i got the Fermi
energy is 6.6632 eVHow is this possible? it must be equal..

please give me your opinion on this query and any suggestion to solve the
problem.

thanks
Dhara raval
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[Pw_forum] Query

[Anindya Bose]

Dear Quantum Espresso experts,
I would like to simulate a hetero-structure of a metallic and an insulating
material,to obtain the band structure using QE,what should be the value of
occupations? Will it be fixed or smearing.Remember the structure is a metal
semiconductor interface.

Thanks and regards,
Anindya Bose
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Re: [Pw_forum] query

[Pietro Delugas]

in your input you set ATOMIC_POSITIONS(crystal) but if I have understood 
well your coordinates are cartesian in angstrom.


In this case you should set ATOMIC_POSITION{angstrom}

Pietro

On 23/05/2017 07:30, aprat...@iisermohali.ac.in wrote:

Hi,
I am trying to run bandstructure calculation for phosphorene sheet using
Quantum Espresso,


Phosphorene has orthorhomic lattice space group =4 So as per QE manual i
kept ibrav=4

a=3.3136A, b=10.478A, c=4.3763A

and four P atoms of unit cell only in Angstroms


But it showing error in reading atomic positions. So, kindly check the
attached input and output file and suggest.


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Re: [Pw_forum] Query about celldm(3)

[GAUTAM SHARMA]

*Take*
*CELL_PARAMETERS from final scf cycle.*


Regards,
Gautam Sharma


On Fri, Jul 28, 2017 at 12:56 PM, GAUTAM SHARMA <
gautam.sha...@students.iiserpune.ac.in> wrote:

> Find *CELL_PARAMETERS* in vc-relax.out , You will see *9 components*.
> (a1,a2,a3), (b1,b2,b3), (c1,c2,c3) and One *alat* value = something
> Use a =alat* Sqrt (a1^2 + a2^2 + a3^2)
> and b= alat* Sqrt (b1^2 + b2^2 + b3^2)
> c = alat* Sqrt (c1^2 + c2^2 + c3^2)
> where * means multiply and ^ means square.
> now divide c /a = celldm (3)
>
>
> Regards,
> Gautam Sharma
>
>
> On Fri, Jul 28, 2017 at 12:32 PM, Anindya Bose 
> wrote:
>
>> Dear Sir,
>> Where can I find the updated celldm(3) value after the successful
>> vc-relax?I need to know the information about c/a ratio of a relaxed
>> structure.Please help.
>>
>> Thanks and regards,
>> Anindya Bose
>> Research Fellow,
>> IIIT Allahabad
>>
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>
>
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Re: [Pw_forum] Query about celldm(3)

[GAUTAM SHARMA]

Find *CELL_PARAMETERS* in vc-relax.out , You will see *9 components*.
(a1,a2,a3), (b1,b2,b3), (c1,c2,c3) and One *alat* value = something
Use a =alat* Sqrt (a1^2 + a2^2 + a3^2)
and b= alat* Sqrt (b1^2 + b2^2 + b3^2)
c = alat* Sqrt (c1^2 + c2^2 + c3^2)
where * means multiply and ^ means square.
now divide c /a = celldm (3)


Regards,
Gautam Sharma


On Fri, Jul 28, 2017 at 12:32 PM, Anindya Bose  wrote:

> Dear Sir,
> Where can I find the updated celldm(3) value after the successful
> vc-relax?I need to know the information about c/a ratio of a relaxed
> structure.Please help.
>
> Thanks and regards,
> Anindya Bose
> Research Fellow,
> IIIT Allahabad
>
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[Pw_forum] Query about celldm(3)

[Anindya Bose]

Dear Sir,
Where can I find the updated celldm(3) value after the successful
vc-relax?I need to know the information about c/a ratio of a relaxed
structure.Please help.

Thanks and regards,
Anindya Bose
Research Fellow,
IIIT Allahabad
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Re: [Pw_forum] Query regarding vdW Griemme Correction

[Giuseppe Mattioli]

Dear Shashi Bhusan Mishra

Please read carefully the input manual:

Variable:   vdw_corr

Type:   CHARACTER
Default:'none'
See:london_s6, london_rcut, london_c6, london_rvdw,  
ts_vdw_econv_thr, ts_vdw_isolated, xdm_a1, xdm_a2
Description:
Type of Van der Waals correction. Allowed values:

'grimme-d2', 'Grimme-D2', 'DFT-D', 'dft-d'  :
 Semiempirical Grimme's DFT-D2.
 Optional variables: "london_s6",  
"london_rcut", "london_c6", "london_rvdw",
 S. Grimme, J. Comp. Chem. 27, 1787 (2006),  
doi:10.1002/jcc.20495
 V. Barone et al., J. Comp. Chem. 30, 934  
(2009), doi:10.1002/jcc.21112

'TS', 'ts', 'ts-vdw', 'ts-vdW', 'tkatchenko-scheffler' :
 Tkatchenko-Scheffler dispersion corrections  
with first-principle derived
 C6 coefficients (implemented in CP only).
 Optional variables: "ts_vdw_econv_thr",  
"ts_vdw_isolated"
 See A. Tkatchenko and M. Scheffler, PRL 102,  
073005 (2009).

'XDM', 'xdm' :
 Exchange-hole dipole-moment model. Optional  
variables: "xdm_a1", "xdm_a2"
 A. D. Becke et al., J. Chem. Phys. 127,  
154108 (2007), doi:10.1063/1.2795701
 A. Otero de la Roza et al., J. Chem. Phys.  
136, 174109 (2012),
 doi:10.1063/1.4705760

Note that non-local functionals (eg vdw-DF) are  
NOT specified here but in "input_dft"

Therefore, if you want to use the sempiempirical Grimme's DFT-D2  
correction you should *only* put

vdw_corr='grimme-d2'

in your input file. vdw-df refers to a *different* family of non-local  
ab initio functionals for the calculation of dispersion forces. Its  
use is *alternative* to the use of DFT-D2-

HTH
Giuseppe

Quoting shashi bhusan mishra :

> Dear Users,
>I have a confusion about adding van der waal's grimme correction
> to my system. In my system I have put a adsorbate layer on top of a
> substrate, the distance of separation is around 4 angstrom but when I add
> vdw correction the separation decreases to 3.2 angstrom. With inclusion of
> only vdW interaction, I got the separation and the adsorption energy.
> However, I need to add Grimme D2 type vdW correction. Do I need to write
>
> ​
> input_dft='vdw-DF'
>   vdw_corr = 'Grimme-D2'​
>
> oronly the correction: vdw_corr= 'Grimme-D2' without mention input dft.
> I am attaching the input file. Please, let me know correction inclusion of
> grimme vdW correction. This varition leads to differnt separation as well
> as adsorption energy.
>
>
> Thanks and regards,
>
> Shashi Bhusan Mi
> ​shra​
>
> Research Scholar,
> ​
> ​
> Dept.
> ​o​
> f Physics,
> IIT Madras-36
>
>
>
>
> ​​


-- 

- Article premier - Les hommes naissent et demeurent
libres et égaux en droits. Les distinctions sociales
ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.


Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: 
http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
ResearcherID: F-6308-2012


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[Pw_forum] Query regarding vdW Griemme Correction

[shashi bhusan mishra]

Dear Users,
   I have a confusion about adding van der waal's grimme correction
to my system. In my system I have put a adsorbate layer on top of a
substrate, the distance of separation is around 4 angstrom but when I add
vdw correction the separation decreases to 3.2 angstrom. With inclusion of
only vdW interaction, I got the separation and the adsorption energy.
However, I need to add Grimme D2 type vdW correction. Do I need to write

​
input_dft='vdw-DF'
  vdw_corr = 'Grimme-D2'​

oronly the correction: vdw_corr= 'Grimme-D2' without mention input dft.
I am attaching the input file. Please, let me know correction inclusion of
grimme vdW correction. This varition leads to differnt separation as well
as adsorption energy.


Thanks and regards,

Shashi Bhusan Mi
​shra​

Research Scholar,
​
​
Dept.
​o​
f Physics,
IIT Madras-36




​​


scf.in
Description: Binary data
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Re: [Pw_forum] query

[Giovanni Cantele]

> On 25 May 2017, at 12:08, aprat...@iisermohali.ac.in wrote:
> 
> Hi,
> I am beginner in using Quantum Espresso. I am giving coordinates of one
> atom (Si 0.0 0.0 0.0) in angstrom/crystal.
> With ibrav=1 it forms Simple Cubic
> With ibrav=2 it forms Face Centred Cubic
> With ibrav=3 it forms Body Centred  Cubic
> and with ibrav=1 and
> Si 0.0 0.0 0.0
> Si 5.0 5.0 0.0
> Si 5.0 0.0 5.0
> Si 0.0 5.0 5.0
> 
> it forms face centred lattice. I would like to know the algorithim which
> Xcrysden follows during visualization?
> 
> what if I want to control the no of atoms 3 or 4 in a Unit cell. ?
> 
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Maybe in the last for positions you meant 0.5, not 5.0. By the way, there is no 
algorithm, but simply at each ibrav
corresponds a lattice. For example ibrav=1 corresponds to a simple cubic 
lattice. The list of ibrav <-> lattice
correspondences can be found here:
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm140629872541472
 


It is true that the lattice sites of a face centered lattice can be described, 
besides using the obvious face centred lattice,
with a simple cubic lattice with four atoms in the unit cell.

I suggest you to read the relevant documentation/tutorials that are available.

Giovanni

-- 

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.fisica.unina.it/~cantele

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[Pw_forum] query

[aprateek]

Hi,
I am beginner in using Quantum Espresso. I am giving coordinates of one
atom (Si 0.0 0.0 0.0) in angstrom/crystal.
With ibrav=1 it forms Simple Cubic
With ibrav=2 it forms Face Centred Cubic
With ibrav=3 it forms Body Centred  Cubic
and with ibrav=1 and
Si 0.0 0.0 0.0
Si 5.0 5.0 0.0
Si 5.0 0.0 5.0
Si 0.0 5.0 5.0

it forms face centred lattice. I would like to know the algorithim which
Xcrysden follows during visualization?

what if I want to control the no of atoms 3 or 4 in a Unit cell. ?

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Re: [Pw_forum] query

[Paolo Giannozzi]

Leave a space between ATOMIC_POSITIONS and {crystal}

P.

On Tue, May 23, 2017 at 7:30 AM,   wrote:
> Hi,
> I am trying to run bandstructure calculation for phosphorene sheet using
> Quantum Espresso,
>
>
> Phosphorene has orthorhomic lattice space group =4 So as per QE manual i
> kept ibrav=4
>
> a=3.3136A, b=10.478A, c=4.3763A
>
> and four P atoms of unit cell only in Angstroms
>
>
> But it showing error in reading atomic positions. So, kindly check the
> attached input and output file and suggest.
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] query

[Duc-Long Nguyen]

On 05/23/2017 01:30 PM, aprat...@iisermohali.ac.in wrote:
> and four P atoms of unit cell only in Angstroms

Then you may considering to put ATOMIC_POSITIONS in Angstrom not 
{crystal}. You can check your unit cell first with xcrysden.
I'm not so familiar with your system but your k-point mesh may not very 
accurate with respect to your unit cell.
(4x4x1 k-mesh when b is the longest lattice parameter).

Best regards,
Duc-Long

-- 

Duc-Long Nguyen
Graduate Student, Molecular Science and Technology Program, TIGP
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan
Phone +886-979279073

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[Pw_forum] query

[aprateek]

Hi,
I am trying to run bandstructure calculation for phosphorene sheet using
Quantum Espresso,


Phosphorene has orthorhomic lattice space group =4 So as per QE manual i
kept ibrav=4

a=3.3136A, b=10.478A, c=4.3763A

and four P atoms of unit cell only in Angstroms


But it showing error in reading atomic positions. So, kindly check the
attached input and output file and suggest.

p-scf-test.in
Description: Binary data


p-scf-test.out
Description: Binary data
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Re: [Pw_forum] query about qexml.f90

[Paolo Giannozzi]

It was moved to a more appropriate place (Modules/qexml.f90)

On Mon, Oct 24, 2016 at 10:21 PM, Kim, Minjung  wrote:

> Dear users,
>
>
>
> I wrote a post-processing script that utilizes qexml module. Recently, I
> realized that qexml.f90 was removed from PP/src directory since version 5.1.
>
> I was wondering if there is a way that I can use qexml module with later
> versions. (And I’m also curious why it had been removed from the package.)
>
> I would appreciate any help.
>
>
>
> Regards,
>
> Minjung Kim
>
>
>
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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] query about qexml.f90

[Kim, Minjung]

Dear users,

I wrote a post-processing script that utilizes qexml module. Recently, I 
realized that qexml.f90 was removed from PP/src directory since version 5.1.
I was wondering if there is a way that I can use qexml module with later 
versions. (And I’m also curious why it had been removed from the package.)
I would appreciate any help.

Regards,
Minjung Kim

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Re: [Pw_forum] Query during Fermi surface calculation

[Goranka Bilalbegovic]

On Tuesday, 1 December 2015, Giovanni Cantele 
wrote:

> If your output file(s) do not show any error message, it looks like an
> error (to much memory used? wall clock limit exceeded in the case you use a
> queuing program? …) coming from the operating system, not from QE.
>
> Usually, when you just find the output cut at some point with no apparent
> reason, it is not du to QE failure. Difficult to say more without further
> information.
>
> On which computer are you doing the calculation?
>
> Giovanni
>
> > On 01 Dec 2015, at 10:10, nirav msc  > wrote:
> >
> > Hello everyone,
> >
> > Kindly reply your suggestions or any help for the said problem.
> >
> > Your help will be highly appreciated.
> >
> >
> > Thanking you,
> > Nirav Pandya,
> >
> > Ph.D. Student
> >
> > India
> > - Forwarded Message -
> > From: nirav msc >
> > To: PWSCF Forum >
> > Sent: Wednesday, 25 November 2015 5:59 PM
> > Subject: Query during Fermi surface calculation
> >
> > Dear QE users and Developers,
> >
> > I am trying to calculate the fermi surface for my system by following
> the steps mentioned in example 8. I am using esspresso 5.0.2.
> >
> > First I have done scf calculation, then generates the k-points by
> kvecs_FS.x for preparing input file for nscf calculation and then run the
> nscf calculation by preparing Sysname.fs_sp.in as below:
> >
> > mpirun -np 4 pw.x -in sysname.fs_sp.in> sysname.fs_sp.out
> >
> > run is going to complete after approximately 20-24 hours.
> >
> > I am not getting any error but output file sysname.fs_sp.out does not
> provide band calculation for all the k-points and it stops. it does not
> provide any band energies and occupation number. last part of the output
> file is given below.
> >
> > Starting wfc are   24 randomized atomic wfcs
> >
> >  total cpu time spent up to now is7.1 secs
> >
> >  per-process dynamical memory:40.0 Mb
> >
> >  Band Structure Calculation
> >  Davidson diagonalization with overlap
> >
> >  Computing kpt #: 1
> >  total cpu time spent up to now is8.3 secs
> >
> >  Computing kpt #: 2
> >  total cpu time spent up to now is9.9 secs
> >
> >  Computing kpt #: 3
> >
> > For your reference input file is given below:
> >
> > 
> > calculation='nscf'
> > restart_mode='from_scratch',
> > tstress = .true.
> > tprnfor = .true.
> > verbosity= 'high'
> > prefix='Sys_name',
> > wf_collect=.true.,
> > pseudo_dir = '/usr/share/espresso/pseudo/',
> > outdir='/tmp/'
> >  /
> >  
> > ibrav= 2, celldm(1)= 10.5615, nat=4,ntyp=2,
> > ecutwfc =80, ecutrho= 800, nbnd=29
> > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01
> > nspin=2,
> > starting_magnetization(1)=0.3, starting_magnetization(2)=0.1
> >  /
> >  
> > conv_thr =  1.0d-5
> > mixing_beta = 0.1
> >  /
> > ATOMIC_SPECIES
> >  atom 1  55.845  Fe.pbe-nd-rrkjus.UPF
> >  atom 2  58.6934 Ni.pbe-nd-rrkjus.UPF
> > ATOMIC_POSITIONS
> > atom 1 0.00 0.00 0.00
> > atom 1 0.25 0.25 0.25
> > atom 1 0.50 0.50 0.50
> > atom 2 0.75 0.75 0.75
> >
> > K_POINTS
> > 4913
> >
> > kindly provide your suggestions or corrections for the same. Your help
> will be highly appreciated.
> >
> > Thanking you,
> > Nirav Pandya,
> >
> > Ph.D. Student
> >
> > India
> >
> >
> > ___
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> > 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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-- 
Goranka Bilalbegovic
Department of Physics, Faculty of Science,
University of Zagreb, Croatia
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[Pw_forum] Query during Fermi surface calculation

[nirav msc]

Dear QE users and Developers,
I am trying to calculate the fermi surface for my system by following the steps 
mentioned in example 8. I am using esspresso 5.0.2. 

First I have done scf calculation, then generates the k-points by kvecs_FS.x 
for preparing input file for nscf calculation and then run the nscf calculation 
by preparing Sysname.fs_sp.in as below:

mpirun -np 4 pw.x -in sysname.fs_sp.in> sysname.fs_sp.out
run is going to complete after approximately 20-24 hours.
 I am not getting any error but output file sysname.fs_sp.out does not provide 
band calculation for all the k-points and it stops. it does not provide any 
band energies and occupation number. last part of the output file is given 
below.
Starting wfc are   24 randomized atomic wfcs

 total cpu time spent up to now is    7.1 secs

 per-process dynamical memory:    40.0 Mb

 Band Structure Calculation
 Davidson diagonalization with overlap

 Computing kpt #: 1
 total cpu time spent up to now is    8.3 secs

 Computing kpt #: 2
 total cpu time spent up to now is    9.9 secs

 Computing kpt #: 3
For your reference input file is given below:

    calculation='nscf'
    restart_mode='from_scratch',
    tstress = .true.
    tprnfor = .true.
    verbosity= 'high'
    prefix='Sys_name',
    wf_collect=.true.,
    pseudo_dir = '/usr/share/espresso/pseudo/',
    outdir='/tmp/'
 /
 
    ibrav= 2, celldm(1)= 10.5615, nat=4,ntyp=2,
    ecutwfc =80, ecutrho= 800, nbnd=29
    occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01
    nspin=2,
    starting_magnetization(1)=0.3, starting_magnetization(2)=0.1
 /
 
    conv_thr =  1.0d-5
    mixing_beta = 0.1
 /
ATOMIC_SPECIES
 atom 1  55.845  Fe.pbe-nd-rrkjus.UPF
 atom 2  58.6934 Ni.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS 
atom 1 0.00 0.00 0.00   
atom 1 0.25 0.25 0.25 
atom 1 0.50 0.50 0.50
atom 2 0.75 0.75 0.75

K_POINTS
4913
kindly provide your suggestions or corrections for the same. Your help will be 
highly appreciated.
Thanking you, 
Nirav Pandya, 

Ph.D. Student
India
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Re: [Pw_forum] Query during VC-relax calculation

[Paolo Giannozzi]

You did not get any error "that was visible to you". In parallel execution,
the worst errors are those you do not see. There can be many reasons why a
parallel code hangs. First of all, try a newer version of QE

Paolo


On Fri, Nov 6, 2015 at 3:37 PM, nirav msc  wrote:

> Dear QE users and Developers,
>
> I am finding the problem during the vc-relax calculation of my material.
> vc-relax calculation is going to hang after generating total energy for few
> number of iterations and then after no further progress is observed in
> output file of the calculation; while the output of "top" command shows the
> running of all the 4 processors (means no termination of the given job).
>
> I did not get any error during the given job.  I am using 5.0.2 version
> of espresso and I am running my calculation by using below command
>
> mpirun -np 4 pw.x -in FeNi.vcr.in> FeNi.vcr.out
>
> Anyone kindly suggest the solution or suggestions for the same? Your help
> will be highly appreciated.
>
> For your reference input file is given below.
>
> 
> calculation = 'vc-relax'
> restart_mode = 'from_scratch' ,
> prefix='FeNi',
> outdir='/tmp/' ,
> pseudo_dir = '/usr/share/espresso/pseudo/',
> disk_io = 'default' ,
> verbosity = 'default' ,
> nstep=300
> etot_conv_thr=1.0E-5
> forc_conv_thr=1.0D-4
> iprint = 10
> tstress = .true. ,
> tprnfor = .true. ,
> max_seconds=12
> dt=20
>  /
>  
>ibrav=0, nat=2, ntyp= 2,
> ecutwfc= 50, ecutrho=500
> occupations='smearing', smearing='m-v', degauss=0.01,
> nspin =2
> starting_magnetization(1)=0.1, starting_magnetization(2)=0.1
> lda_plus_u=.false.
>  /
>  
> diagonalization='david'
> mixing_mode = 'plain'
> mixing_beta = 0.1
> conv_thr =  1.0d-5
> electron_maxstep=200
>  /
> 
> /
> 
> cell_dynamics='damp-w'
> press=0
> wmass=0.0070
> /
> CELL_PARAMETERS Hexagonal
> 13.000 0. 0.
> 0. 13.000 0.
> 0. 0. 18.382
>
> ATOMIC_SPECIES
> Fe  1  Fe.pbe-nd-rrkjus.UPF
> Ni  1  Ni.pbe-nd-rrkjus.UPF
>
> ATOMIC_POSITIONS alat
> Fe 0.0 0.0 0.0
> Ni 0.5 0.5 0.5
>
> K_POINTS automatic
> 4 4 4 1 1 1
>
>
> Thanks
>
>
>
> Nirav Pandya,
>
> Ph.D. student
>
> India
>
>
>
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>



-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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[Pw_forum] Query during VC-relax calculation

[nirav msc]

Dear QE users and Developers,
I am finding the problem during the vc-relax calculation of my material. 
vc-relax calculation is going to hang after generating total energy for few 
number of iterations and then after no further progress is observed in output 
file of the calculation; while the output of "top" command shows the running of 
all the 4 processors (means no termination of the given job). 

I did not get any error during the given job.  I am using 5.0.2 version of 
espresso and I am running my calculation by using below command
mpirun -np 4 pw.x -in FeNi.vcr.in> FeNi.vcr.out
Anyone kindly suggest the solution or suggestions for the same? Your help will 
be highly appreciated.

For your reference input file is given below.


    calculation = 'vc-relax'
    restart_mode = 'from_scratch' ,    prefix='FeNi',
    outdir='/tmp/' ,
    pseudo_dir = '/usr/share/espresso/pseudo/',
    disk_io = 'default' ,
    verbosity = 'default' ,
    nstep=300
    etot_conv_thr=1.0E-5
    forc_conv_thr=1.0D-4
    iprint = 10
    tstress = .true. ,
    tprnfor = .true. ,
    max_seconds=12
    dt=20
 /
 
   ibrav=0, nat=2, ntyp= 2,
    ecutwfc= 50, ecutrho=500
    occupations='smearing', smearing='m-v', degauss=0.01,
    nspin =2
    starting_magnetization(1)=0.1, starting_magnetization(2)=0.1
    lda_plus_u=.false.
 /
 
    diagonalization='david'
    mixing_mode = 'plain'
    mixing_beta = 0.1
    conv_thr =  1.0d-5
    electron_maxstep=200
 /

/

cell_dynamics='damp-w'
press=0
wmass=0.0070
/
CELL_PARAMETERS Hexagonal
13.000 0. 0.
0. 13.000 0.
0. 0. 18.382
ATOMIC_SPECIES
Fe  1  Fe.pbe-nd-rrkjus.UPF
Ni  1  Ni.pbe-nd-rrkjus.UPF 
ATOMIC_POSITIONS alat
Fe 0.0 0.0 0.0  
Ni 0.5 0.5 0.5
K_POINTS automatic
4 4 4 1 1 1 

Thanks 

 
Nirav Pandya, 

Ph.D. student
India
   
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[Pw_forum] Query on Double numerical atomic orbitals

[Nicola Marzari]

Dear Ajit,


it's a completely different story - QE uses plane waves as a basis
set, and you just increase the cutoff to improve your basis convergence.

Other codes (quantum chemistry codes, SIESTA...) use atomic-like or 
gaussian-like localized basis sets; you need much fewer of these, but
convergence is much trickier.

You probably need to study a good book on electronic structure methods,
and/or some of the tutorials on the QE webpage, before doing much else.

nicola



On 09/01/2014 05:23, Ajit Vallabhaneni wrote:
> Dear QE users,
>
>I am new to QE and am trying to do some calculations on GNRs. In 
> the literature i reviewed, it was mentioned that "double numerical atomic 
> orbitals along with polarisation functions" were used as a basis for the tens 
> of atoms in the unitcell. From the little i understood, the double radial 
> functions lead to better accuracy and convergence. I was wondering if it is 
> implemented by default in QE or not. Please let me know.
>
>


-- 

--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

[Pw_forum] Query on Double numerical atomic orbitals

[Ajit Vallabhaneni]

Dear QE users,

  I am new to QE and am trying to do some calculations on GNRs. In the 
literature i reviewed, it was mentioned that "double numerical atomic orbitals 
along with polarisation functions" were used as a basis for the tens of atoms 
in the unitcell. From the little i understood, the double radial functions lead 
to better accuracy and convergence. I was wondering if it is implemented by 
default in QE or not. Please let me know.


-- 
Thank You
Ajit 

[Pw_forum] Query in conductance calculation

[N H Joshi]

Dear all,

I am trying to calculate transmission at a junction consisting of monolayer
of graphene between two same transition metal slabs (TM) using the PWCOND
code. Taking help from the examples discussed on the website (
http://iramis.cea.fr/Pisp/alexander.smogunov/PWCOND/examples.html ) I have
calculated the transmission when the magnetic moment of TM on both the
sides are aligned parallel  and antiparallel to each other.

While doing the calculation for the antiparallel case, two junctions are
present in the scattering region. So the query that I have is, how do I
calculate the transmission value for a single junction in this case?

-- 
Niharika Joshi
Project student,
IISER,Pune
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[Pw_forum] Query in conductance calculation

[Alex Smogunov]

Indeed, in the antiparallel case you should do calculations with ikind=2
and have two files for
left and right leads with up and down magnetizations. In the pwcond input
file you should also specify
the bds value, where the scattering region ends up, it will be in the
middle of the cell used in pw.x calculation.
regards,
Alex



2013/10/31 Gabriele Sclauzero 

> Dear Niharika joshi,
>
> I'm not sure to understand correctly your problem, but I think your
> case is similar to one of the examples on the webpage you mentioned, namely
> "Monatomic Ni wire with a spin reversal". You have to double to unit cell
> (in a specular manner) in the scf calculation of the scattering region,
> then use only the first half in the pwcond calculation.
>
> In both cases there is one "junction", but two "interfaces" (one between
> left lead and scattering region and a second between scattering region and
> right lead).
> The difference is that the leads are the same in the parallel case, while
> they are different in the antiparallel one.
> In both cases, what the code computes is what one expects, the conductance
> for the single junction (i.e., for electrons "going" from the left lead to
> the right one through the scattering region).
>
> HTH
>
> GS
>
>
> Dear all,
>
> I am trying to calculate transmission at a junction consisting of
> monolayer of graphene between two same transition metal slabs (TM) using
> the PWCOND code. Taking help from the examples discussed on the website (
> http://iramis.cea.fr/Pisp/alexander.smogunov/PWCOND/examples.html ) I
> have calculated the transmission when the magnetic moment of TM on both the
> sides are aligned parallel  and antiparallel to each other.
>
> While doing the calculation for the antiparallel case, two junctions are
> present in the scattering region. So the query that I have is, how do I
> calculate the transmission value for a single junction in this case?
>
> --
> Niharika Joshi
> Project student,
> IISER,Pune
>  ___
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> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
> ___
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>
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[Pw_forum] Query in conductance calculation

[Gabriele Sclauzero]

Dear Niharika joshi,

I'm not sure to understand correctly your problem, but I think your case is 
similar to one of the examples on the webpage you mentioned, namely "Monatomic 
Ni wire with a spin reversal". You have to double to unit cell (in a specular 
manner) in the scf calculation of the scattering region, then use only the 
first half in the pwcond calculation.

In both cases there is one "junction", but two "interfaces" (one between left 
lead and scattering region and a second between scattering region and right 
lead).
The difference is that the leads are the same in the parallel case, while they 
are different in the antiparallel one.
In both cases, what the code computes is what one expects, the conductance for 
the single junction (i.e., for electrons "going" from the left lead to the 
right one through the scattering region).

HTH

GS


> Dear all,
> 
> I am trying to calculate transmission at a junction consisting of monolayer 
> of graphene between two same transition metal slabs (TM) using the PWCOND 
> code. Taking help from the examples discussed on the website ( 
> http://iramis.cea.fr/Pisp/alexander.smogunov/PWCOND/examples.html ) I have 
> calculated the transmission when the magnetic moment of TM on both the sides 
> are aligned parallel  and antiparallel to each other.
> 
> While doing the calculation for the antiparallel case, two junctions are 
> present in the scattering region. So the query that I have is, how do I 
> calculate the transmission value for a single junction in this case?
> 
> -- 
> Niharika Joshi
> Project student, 
> IISER,Pune
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum


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

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[Pw_forum] query on kpoints.x

[Paolo Giannozzi]

On Wed, 2012-04-25 at 02:10 -0400, Ajit Vallabhaneni wrote:

> I want to know whether the format for k points output by kpoints.x 
> is tpiba or not ? 

I think so. This is something you can easily verify

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

[Pw_forum] query on kpoints.x

[Ajit Vallabhaneni]

Dear users,

I want to know whether the format for k points output by kpoints.x 
is tpiba or not ? 


Thanks
Ajit

[Pw_forum] Query on band crossing

[Paolo Giannozzi]

On Fri, 2012-04-13 at 04:25 -0400, Ajit Vallabhaneni wrote:

>  In the scf output, the energies at every K point
>  are arranged from lowest to highest. I want to know 
> if that order holds true in el-ph calculations as well

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

[Pw_forum] Query on band crossing

[Ajit Vallabhaneni]

Dr. Marzari,


I have a question regarding the order of the bands in the scf and 
elph calculations. In the scf output, the energies at every K point
 are arranged from lowest to highest. I want to know if that order holds true 
in el-ph calculations as well. Like in elphon.f90 file, the variables ibnd,jbnd 
vary from 1 to nbnd; do they have the same increasing order as in the scf ? 


Thanks
Ajit

[Pw_forum] Query on band crossing

[Nicola Marzari]

Dear Ajit,


it's not a trivial question to answer; probably the best solution is to
use Wannier functions as interpolators - see e.g. the
discussion here (http://arxiv.org/abs/1112.5411).

nicola



On 11/04/2012 06:06, Ajit Vallabhaneni wrote:
> Dear Users and developers,
>
>   I have a question regarding the crossing of branches in 
> electron and phonon dispersion plots. Since the no. of elec bands vary from 1 
> to nbnd and phonon branches vary from 1 to 3*nat, in the output files they 
> are written usually from the minimum to maximum.
>
> I want to make sure whether for different points in the BZ, the bands are 
> always considered in the same order (from min to max) without considering any 
> crossing of bands in both scf and also e-ph calculations. What is the best 
> way to distinguish or track one band across the entire BZ? I believe for 
> phonons, the eigen vectors could help to some extent, then what about 
> electrons?
>
>
> Thanks
> Ajit
>
>
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

[Pw_forum] Query on band crossing

[Ajit Vallabhaneni]

Dear Users and developers,

 I have a question regarding the crossing of branches in 
electron and phonon dispersion plots. Since the no. of elec bands vary from 1 
to nbnd and phonon branches vary from 1 to 3*nat, in the output files they are 
written usually from the minimum to maximum. 

   I want to make sure whether for different points in the BZ, the bands are 
always considered in the same order (from min to max) without considering any 
crossing of bands in both scf and also e-ph calculations. What is the best way 
to distinguish or track one band across the entire BZ? I believe for phonons, 
the eigen vectors could help to some extent, then what about electrons? 


Thanks
Ajit


 

[Pw_forum] query on e-ph tutorial

[GAO Zhe]

This problem happens during diagonalize the matrix. At least there are two 
methods to solve this problem: Firstly, changing the diagonalization method to 
CG, which requires to modify the PH code; secondly, increasing empty bands by 
"nbnd" parameter in the input file of pw.x.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 



At 2012-01-30 22:48:10,"Ajit Vallabhaneni"  wrote:
>Dear Paolo,
>
>Sorry for sending my response to your personal email. I didn't 
> see it before.Here is my question.
>
> I tried example 7 with the same parameters given. But the 
> al.elph.in (with nq1=nq2=nq3=4) was terminated with the following message: 
>
>
>Band Structure Calculation
> Davidson diagonalization with overlap
>
> %%
> from cdiaghg : error #19
> diagonalization (ZHEGV*) failed
> %%
>
> stopping ...
>
>
>Is this because of the small mesh size (16x16x16)?
>
>Thanks
>Ajit
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[Pw_forum] query on e-ph tutorial

[Ajit Vallabhaneni]

Dear Paolo,

Sorry for sending my response to your personal email. I didn't 
see it before.Here is my question.

 I tried example 7 with the same parameters given. But the 
al.elph.in (with nq1=nq2=nq3=4) was terminated with the following message: 


Band Structure Calculation
 Davidson diagonalization with overlap

 %%
 from cdiaghg : error #19
 diagonalization (ZHEGV*) failed
 %%

 stopping ...


Is this because of the small mesh size (16x16x16)?

Thanks
Ajit

[Pw_forum] query on e-ph tutorial

[Paolo Giannozzi]

On Jan 29, 2012, at 7:30 , Ajit Vallabhaneni wrote:

> I mean will calculating those quantities across the IBZ sufficient
> to obtain the values thru out the entire BZ?

I don't think so: at a given q, you can sum over the IBZ of the small
group of q and symmetrize with the small group of q, or else, if you
sum over the IBZ of the symmetry group, you will need the unsymmetrized
quantity for all q vectors in the star of q.

> 2. In the tutorial on for calculating the "Electron-phonon  
> interaction coefficients"
> on the website of QE (http://www.fisica.uniud.it/~giannozz/QE- 
> Tutorial/tutorial_advph.html)

it is not "the website of QE": it is my website, where I keep a copy  
of some
files often used in tutorials. Unfortunately that part is obsolete.  
You should
look at the example 07.

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

[Pw_forum] query on e-ph tutorial

[Ajit Vallabhaneni]

Dear users,


I have a couple of questions regarding the e-ph calculation.
1. Are the e-ph matrix element (g), coefficients lambda and gamma symmetric 
with respect to the phonon wave vector (q)? I mean will calculating those 
quantities across the IBZ sufficient to obtain the values thru out the entire 
BZ? 

2. In the tutorial on for calculating the "Electron-phonon interaction 
coefficients" on the website of QE 
(http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html), in step 
3 it was mentioned to perform an nscf calculation to prepare k and k+q 
wavefunctions with the keyword "calculation='phonon'". I tried to run the same, 
but it was termintated with the message that calculation "phonon" is not 
allowed. Are there any typos in this part of the example.

-bash-3.2$ pw.x < al.nscf.in

 Program PWSCF v.4.3.2  starts on 29Jan2012 at  1:21:57

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL http://www.quantum-espresso.org;,
 in publications or presentations arising from this work. More details at
 http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

 Parallel version (MPI), running on 1 processors

 Current dimensions of program PWSCF are:
 Max number of different atomic species (ntypx) = 10
 Max number of k-points (npk) =  4
 Max angular momentum in pseudopotentials (lmaxx) =  3
 Waiting for input...
 Reading input from stdin

 %%
 from  control_checkin : error # 1
  calculation 'phonon' not allowed
 %%

 stopping ...
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0



Thanks
Ajit

[Pw_forum] query on fermi energy

[Paolo Giannozzi]

On Jan 16, 2012, at 19:06 , Ajit Vallabhaneni wrote:

>  Sorry i didnot understand your question.

I don' understand why you insist that something is not
working and don't provide any evidence.

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

[Pw_forum] query on fermi energy

[Ajit Vallabhaneni]

Dr.Paolo,

 Sorry i didnot understand your question.

Thanks
Ajit

[Pw_forum] query on fermi energy

[Paolo Giannozzi]

On Jan 15, 2012, at 12:50 , Ajit Vallabhaneni wrote:

> I observed that using a dense grid is not enough sometimes

you observed in which case?

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

"Nothing is impossible for the man who doesn't have to do it himself"

[Pw_forum] query on fermi energy

[Ajit Vallabhaneni]

Dr. Paolo,

 Like in graphene, i used 60x60 mesh, but for some q-points it 
terminates with the message that "it is not a part of dense grid".
Should i increase the grid size even more? It is very expensive computationally 
though.

Thanks
Ajit

[Pw_forum] query on fermi energy

[Nicola Marzari]

Dear Peter,

also, there is an example in the qe distribution on how to calculate 
fermi energies via slab calculations - and there is extensive literature 
- e.g. the PhD thesis of Caspar Fall
http://library.epfl.ch/en/theses/?nr=1955 , or
Phys. Rev. B 80, 235407 (2009).


nicola


On 1/14/12 6:14 PM, Peter Wang wrote:
> if we do a bulk calculation, vacuum energy level can not be calculated,
> because in bulk, there is no vacuum. To calculate vacuum energy level and
> the relative energies in bulk with respect to vacuum energy level, a slab
> calculation should be done. In a slab calculation, several layer of
> materials as well as a vacuum with sufficient thinkness should be included
> in one unit cell.
>
> YP
>
> --
> From: Ajit Vallabhaneni
> Sent: Sunday, January 15, 2012 1:06 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] query on fermi energy
>
> Yun-peng,
>
>   Thanks for your response. Is it possible to know what the vaccum
> energy level is ? I read in the FAQ that it cannot be calculated from the a
> bulk calculation alone.
>
>
> Thanks
> Ajit
> ___
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--
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[Pw_forum] query on fermi energy

[Ajit Vallabhaneni]

   Any thoughts on my second question  regarding the e-ph calculation. 
For a give set of q and k points, what is the best way to ensure that all 
k+q points are available to avoid the message " q is not a vector in the 
dense grid" in the calculations"? I observed that using a dense grid is not 
enough sometimes. Do we have to check it outside of the quantum espresso 
before the calculation begins?
 
Thanks
Ajit

[Pw_forum] query on fermi energy

[Peter Wang]

if we do a bulk calculation, vacuum energy level can not be calculated, 
because in bulk, there is no vacuum. To calculate vacuum energy level and 
the relative energies in bulk with respect to vacuum energy level, a slab 
calculation should be done. In a slab calculation, several layer of 
materials as well as a vacuum with sufficient thinkness should be included 
in one unit cell.

YP

-- 
From: Ajit Vallabhaneni
Sent: Sunday, January 15, 2012 1:06 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] query on fermi energy

Yun-peng,

 Thanks for your response. Is it possible to know what the vaccum 
energy level is ? I read in the FAQ that it cannot be calculated from the a 
bulk calculation alone.


Thanks
Ajit
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[Pw_forum] query on fermi energy

[Peter Wang]

for the first question, there is no absolute Fermi energy. The only absolute 
energy is that substracting vacuum energy level from it.

best
Yun-Peng

-- 
From: Ajit Vallabhaneni
Sent: Saturday, January 14, 2012 3:32 PM
To: PWSCF Forum
Subject: [Pw_forum] query on fermi energy

Dear users,

  1.  I was wondering how to calculate the absolute value of fermi 
energy for graphene single layer. By varying the size of the super cell in 
the out of plane direction, i observed that the total energy is constant 
indicating no  interactions in the out of plane direction, but the fermi 
energy is varying with increasing distance. I think it is the relative fermi 
energy which is output after the scf calculation. I want to know the 
absolute value.


   2.  Another question i have is regarding the e-ph calculation. 
For a give set of q and k points, what is the best way to ensure that all 
k+q points are available to avoid the message " q is not a vector in the 
dense grid" in the calculations"? I observed that using a dense grid is not 
enough sometimes. Do we have to check it outside of the quantum espresso 
before the calculation begins?


Thanks
Ajit
___
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 

[Pw_forum] query on fermi energy

[Ajit Vallabhaneni]

Dear users,

  1.  I was wondering how to calculate the absolute value of fermi 
energy for graphene single layer. By varying the size of the super cell in the 
out of plane direction, i observed that the total energy is constant indicating 
no  interactions in the out of plane direction, but the fermi energy is varying 
with increasing distance. I think it is the relative fermi energy which is 
output after the scf calculation. I want to know the absolute value. 

 
   2.  Another question i have is regarding the e-ph calculation. For a 
give set of q and k points, what is the best way to ensure that all k+q points 
are available to avoid the message " q is not a vector in the dense grid" in 
the calculations"? I observed that using a dense grid is not enough sometimes. 
Do we have to check it outside of the quantum espresso before the calculation 
begins? 


Thanks
Ajit

[Pw_forum] query on k-points with MP

[Ajit Vallabhaneni]

Dear users,

   I am doing some scf calculations with K-points specified by the 
Monkhorst-Pack grid scheme. In the output file,  only the k-points in the IBZ 
are shown. Is there any way i can see all the K-points in the entire BZ? I just 
want to make sure certain K points are included. 


Thanks
Ajit 

[Pw_forum] query on e-ph matrix element

[Hua Bao]

Dear QE-users and Paolo,

Thanks for your explanation.
Actually we can completely understand npert(irr).
However, there is still difficulty for us to relate npert(irr) to a
specific \nu.

When we track the quantity "npert", we could not find out where it is
modified (although we know it is defined in phcom.f90).

Would you please point out the relationship between npert and \nu?
Just point out which files we need to look into will be helpful.

Thanks,
Hua


On Mon, Dec 12, 2011 at 5:44 AM, Paolo Giannozzi wrote:

> On Sun, 2011-12-11 at 00:31 -0500, Ajit Vallabhaneni wrote:
>
> > I had gone thru the source code "elphon.f90" for this purpose.
>
> wow! you are a brave man
>
> > I could figure out all the variables like k,i,j,q but not nu.
> > I see a variable 'imode0' which i cannot figure out its purpose.
> > Can someone please help me with identifying the nu ?
>
> the el-ph matrix elements are calculated for each irrep, i.e.
> displacement patterns transforming into each other under the
> symmetry operations of the small group of each wavevector.
> There are nirr irreps, each having dimension npert(irr).
> The code runs over irreps: irr=1,..,nirr, then over irrep
> components: ipert=1,..,npert(irr), and imode0+ipert is the
> index of each displacement pattern. Only when the el-phon
> coefficient "gamma" is calculated are phonon modes (contained
> in matrix "dyn") actually used.
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
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[Pw_forum] query on e-ph matrix element

[Axel Kohlmeyer]

On Mon, Dec 12, 2011 at 6:44 PM, Ajit Vallabhaneni  
wrote:
> Dear Paolo
>
> ? ? ?Can you please explain what the variable "zdotc" in elphon.f90 exactly 
> does? I think it calculates the derivative of the potential. ?It is declared 
> as an external variable but i couldnot figure out the location it has been 
> calculated. Can you show me the the path as well where it is calculated ?

zdotc is not a variable but a BLAS function:

NAME
   ZDOTC - forms the dot product of a vector

SYNOPSIS
   DOUBLE COMPLEX FUNCTION ZDOTC(N,ZX,INCX,ZY,INCY)

   INTEGERINCX,INCY,N

   DOUBLE COMPLEX ZX(*),ZY(*)

PURPOSE
   ZDOTC forms the dot product of a vector.


please note the difference in the meaning of "external"
between C and Fortran. ;)

cheers,
 axel.

>
> Thanks
> Ajit
> ___
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-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

[Pw_forum] query on e-ph matrix element

[Ajit Vallabhaneni]

Dear Paolo

  Can you please explain what the variable "zdotc" in elphon.f90 exactly 
does? I think it calculates the derivative of the potential.  It is declared as 
an external variable but i couldnot figure out the location it has been 
calculated. Can you show me the the path as well where it is calculated ? 


Thanks
Ajit

[Pw_forum] query on e-ph matrix element

[Paolo Giannozzi]

On Mon, 2011-12-12 at 09:23 -0500, Ajit Vallabhaneni wrote:

> Are you implying that "g" cannot be calculated for a particular
>  phonon (of specific q and nu) ?

no, I am not implying.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

[Pw_forum] query on e-ph matrix element

[Paolo Giannozzi]

On Sun, 2011-12-11 at 00:31 -0500, Ajit Vallabhaneni wrote:

> I had gone thru the source code "elphon.f90" for this purpose.

wow! you are a brave man

> I could figure out all the variables like k,i,j,q but not nu. 
> I see a variable 'imode0' which i cannot figure out its purpose. 
> Can someone please help me with identifying the nu ? 

the el-ph matrix elements are calculated for each irrep, i.e.
displacement patterns transforming into each other under the
symmetry operations of the small group of each wavevector. 
There are nirr irreps, each having dimension npert(irr).
The code runs over irreps: irr=1,..,nirr, then over irrep
components: ipert=1,..,npert(irr), and imode0+ipert is the 
index of each displacement pattern. Only when the el-phon
coefficient "gamma" is calculated are phonon modes (contained 
in matrix "dyn") actually used. 

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

[Pw_forum] query on e-ph matrix element

[Ajit Vallabhaneni]

Dear Paolo,

  Thanks for your response. But i am not sure i understand it 
completely. Are you implying that "g" cannot be calculated for a particular 
phonon (of specific q and nu) ? I am not entirely familiar with the concepts of 
irreducible representation. But in the expression for "g", there is a 
omega_nu,q and also the derivative of V_SCF with respect to displacement along 
a particular nu for a given q. 


Thanks
Ajit

[Pw_forum] query on e-ph matrix element

[Ajit Vallabhaneni]

Dear users,

   I am trying to calculate e-ph matrix element (g) for Aluminium as a 
function of q (phonon wave vector) and nu(index of the phonon branch). I had 
gone thru the source code "elphon.f90" for this purpose. I could figure out all 
the variables like k,i,j,q but not nu. I see a variable 'imode0' which i cannot 
figure out its purpose. Can someone please help me with identifying the nu ? 

Also is there an efficient way to estimate g from the values of lambda and 
gamma ?


Thanks
Ajit

[Pw_forum] Query about O.pbe-rrkjus.UPF Pseudopotential

[Paolo Giannozzi]

On Dec 6, 2011, at 10:58 , Lorenzo Paulatto wrote:

> Hint: if you open it with a tex teditor you'll find this line:
>US  Ultrasoft pseudopotential

further hint: in the pseudopotential page, there is a link to a
page describing the naming convention used for UPF files:
   http://www.quantum-espresso.org/wiki/index.php/ 
Naming_convention_for_the_pseudopotential
P.
---
Paolo Giannozzi, Dept of Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] Query about O.pbe-rrkjus.UPF Pseudopotential

[Lorenzo Paulatto]

In data 06 December 2011 alle ore 10:55:34, Shaptrishi Sharma  
 ha scritto:
> O.pbe-rrkjus.UPFa
> norm conserving pseudopotential or ultrasoft pseudopotential ?

Dear Shaptrishi,
it is ultrasoft.

Hint: if you open it with a tex teditor you'll find this line:
   US  Ultrasoft pseudopotential

best regards


-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

[Pw_forum] Query about O.pbe-rrkjus.UPF Pseudopotential

[Shaptrishi Sharma]

Hi,

is 
O.pbe-rrkjus.UPFa
norm conserving pseudopotential or ultrasoft pseudopotential ?

Best
Shapt

IIT Mumbai
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[Pw_forum] Query on "e-ph interaction coefficients

[Stefano Baroni]

On Nov 28, 2011, at 5:34 PM, Ajit Vallabhaneni wrote:

> Dear Paolo,
> 
>I studied little bit of group theory in the context of algebra a 
> while back.

this is probably not quite enough for your purposes

> Can you please suggest any reference in the present context if possible? 

Group theory used to be a standard component of any graduate course in 
solid-state theory, when I was a student (i.e. quite some time ago). Plenty of 
references on this topic. You may want to start from:

Symmetry in the Solid State, by Knox & Gold
Symmetry principles in solid state and molecular physics, by Lax
Group theory in quantum mechanics, by Heine

or many other titles that you will easily discover by "googling"

HTH - SB

> 
> Thanks
> Ajit
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni 
(skype)

La morale est une logique de l'action comme la logique est une morale de la 
pens?e - Jean Piaget

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[Pw_forum] Query on "e-ph interaction coefficients

[Paolo Giannozzi]

On Nov 28, 2011, at 1:19 , Ajit Vallabhaneni wrote:

> what does the term 1 modes  and 2 modes stand for ?

one-dimensional, two dimensional irreducible representations.
Do you know group theory?

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

[Pw_forum] Query on "e-ph interaction coefficients

[Ajit Vallabhaneni]

Dear Paolo,

I studied little bit of group theory in the context of algebra a 
while back. Can you please suggest any reference in the present context if 
possible? 

Thanks
Ajit

[Pw_forum] Query on "e-ph interaction coefficients

[Ajit Vallabhaneni]

Dear users,

 I had recently started working on Quantum espresso. I was 
doing the tutorials on e-ph interaction coeff's tutorial on aluminium. I ran 
the simulation at point X. The following is a part of the output in which i 
want to know what few things represent. 

- what does the two irreducible representations mean ? It shows that it is 
related to atomic displacements, but i could not see what does the terms 
"Representation  1 1 modes -A_2u X_4' M_4' To be done " means and what does the 
term 1 modes  and 2 modes stand for ?


Thanks
Ajit  
 




 Atomic displacements:
 There are   2 irreducible representations

 Representation 1  1 modes -A_2u X_4' M_4' To be done

 Representation 2  2 modes -E_u  X_5' M_5' To be done


 Representation #  1 mode #   1

 Self-consistent Calculation

  iter #   1 total cpu time :27.1 secs   av.it.:   3.9
  thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.735E-04

  iter #   2 total cpu time :28.0 secs   av.it.:   5.4
  thresh= 0.857E-03 alpha_mix =  0.700 |ddv_scf|^2 =  0.311E-04

  iter #   3 total cpu time :29.0 secs   av.it.:   5.1
  thresh= 0.558E-03 alpha_mix =  0.700 |ddv_scf|^2 =  0.526E-08

  iter #   4 total cpu time :29.9 secs   av.it.:   5.4
  thresh= 0.725E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.289E-10

  iter #   5 total cpu time :30.8 secs   av.it.:   5.1
  thresh= 0.537E-06 alpha_mix =  0.700 |ddv_scf|^2 =  0.779E-14

 End of self-consistent calculation

 Convergence has been achieved 


 Representation #  2 modes #   2  3

 Self-consistent Calculation

  iter #   1 total cpu time :33.4 secs   av.it.:   3.5
  thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.298E-06

  iter #   2 total cpu time :35.4 secs   av.it.:   6.2
  thresh= 0.546E-04 alpha_mix =  0.700 |ddv_scf|^2 =  0.406E-08

  iter #   3 total cpu time :37.3 secs   av.it.:   5.7
  thresh= 0.637E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.401E-09

  iter #   4 total cpu time :39.2 secs   av.it.:   5.5
  thresh= 0.200E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.119E-13

  iter #   5 total cpu time :41.3 secs   av.it.:   6.4
  thresh= 0.109E-07 alpha_mix =  0.700 |ddv_scf|^2 =  0.471E-15

 End of self-consistent calculation

 Convergence has been achieved 
 
 Number of q in the star =3
 List of q in the star:
  1   0.0   0.0   1.0
  2   0.0   1.0   0.0
  3   1.0   0.0   0.0

 Diagonalizing the dynamical matrix

 q = (0.0   0.0   1.0 ) 

 **
 omega( 1) =   6.001070 [THz] = 200.174161 [cm-1]
 omega( 2) =   6.001070 [THz] = 200.174161 [cm-1]
 omega( 3) =   9.595361 [THz] = 320.066785 [cm-1]
 **

 Mode symmetry, D_4h(4/mmm) point group:

 omega(  1 -  2) =200.2  [cm-1]   --> E_u  X_5' M_5' 
 omega(  3 -  3) =320.1  [cm-1]   --> A_2u X_4' M_4' 

 **

[Pw_forum] Query on phonon dispersion

[Paolo Giannozzi]

On Nov 20, 2011, at 21:51 , Ajit Vallabhaneni wrote:

> " iii) In specifying the k-space coordinates to obtain frequencies
> at a point in the file "*.matdyn.in", what are the units for the co- 
> ordinates?

2pi/a (it is written in the header of file matdyn.f90)

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

[Pw_forum] Query on phonon dispersion

[Lorenzo Paulatto]

In data 20 novembre 2011 alle ore 18:56:27, Ajit Vallabhaneni  
 ha scritto:
> I want to know the answer for the following questions as well

There is a lot of literature on the subject, please have a look at:
Phys. Rev. B 71, 205214
Phys. Rev. Lett. 93, 185503
Phys. Rev. Lett. 99, 176802


where all your question are answered (if I forgot something, feel free to  
come back to us)

best regards

-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

[Pw_forum] Query on phonon dispersion

[Ajit Vallabhaneni]

Paulatto,

Thanks for your quick reply. But i still have doubts on my third 
question. It's more of a programming question which cannot be found in journal 
papers.

" iii) In specifying the k-space coordinates to obtain frequencies at a point 
in the file "*.matdyn.in", what are the units for the co-ordinates? are they 
just (2*pi/alat) or crystal (in terms of reciprocal lattice vectors)? "

 Also do you have experience on graphene? 

Thanks
Ajit

[Pw_forum] Query on "e-ph coupling"

[Ajit Vallabhaneni]

Never mind, i figured that out myself. 


Thanks
Ajit

[Pw_forum] Query on "e-ph coupling"

[Ajit Vallabhaneni]

 From the tutorials, i have seen that "g" is needed for the calculation of 
" gamma". I just want to know whether the term "g" is internally being 
calculated or not. So do i just have to make changes to the code to print it or 
write code separately?

Thanks
Ajit

[Pw_forum] Query on Xcrysden

[Huiqun Zhou]

When you try to use XCrysden from PWgui, you still need to have a copy of
XCrysden to be installed in advance.


dr. zhou huiqun
@earth sciences, nanjing university, china

- Original Message - 
From: "Ren PJ" <re...@dicp.ac.cn>
To: 
Sent: Monday, November 07, 2011 10:50 PM
Subject: Re: [Pw_forum] Query on Xcrysden


> 
> There is a executable file which need not to install. The latest version
> is 4.3. The url is: http://www-k3.ijs.si/kokalj/pwgui/
> 
> 
> 
> 
> Pengju Ren
> renpj at dicp.ac.cn
> State  Key Laboratory of Catalysis, 
> Dalian Institute of Chemical Physics, 
> Chinese Academy of Sciences 
> 457 zhongshan Road, Dalian, 116023, P.R. China  
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] Query on "e-ph coupling"

[Paolo Giannozzi]

On Tue, 2011-11-08 at 12:06 -0500, Ajit Vallabhaneni wrote:

> I had recently gone through the tutorials on e-ph coupling for Al.
>  I am able to get the values of lambda and gamma from the program 
> but it was not clear to me how to get the value of the matrix element
>  "g" from that.

if you are referring to the matrix element of the electron-phonon
coupling, <\psi|dV/du|\psi>, you have to go inside the code to get it

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

[Pw_forum] Query on "e-ph coupling"

[Ajit Vallabhaneni]

Dear users,

  I had recently gone through the tutorials on e-ph coupling for Al. I 
am able to get the values of lambda and gamma from the program but it was not 
clear to me how to get the value of the matrix element "g" from that. Can 
someone please help me with this?

Thanks
Ajit

[Pw_forum] Query on Xcrysden

[Ren PJ]

There is a executable file which need not to install. The latest version
is 4.3. The url is: http://www-k3.ijs.si/kokalj/pwgui/




Pengju Ren
renpj at dicp.ac.cn
State  Key Laboratory of Catalysis, 
Dalian Institute of Chemical Physics, 
Chinese Academy of Sciences 
457 zhongshan Road, Dalian, 116023, P.R. China  

[Pw_forum] Query on Xcrysden

[Ajit Vallabhaneni]

Dear users,
 
I am a new user of QE. I installed QE 4.3.1 and trying to repeat 
the simulations shown in the tutorials 
(http://www.fisica.uniud.it/~giannozz/QE-Tutorial/). Also i had some 
compatibility issues with my Linux environment and i cannot install the latest 
version of xcrysden for visualisation. I can only use the older version (V1.4). 
I want to know whether this older version is totally compatible with the QE 
version or not. Because i am not able to see the output files of the PWSCF 
calculations. Like for the file si.scf.in i am able to see the initial 
structure but not the output file si.scf.out.

 ERROR: while executing exec sh
 ERROR INFO: Child process exited abnormally


Thanks
Ajit

[Pw_forum] Query regarding real space interatomic force constant

[Stefano Baroni]

Dear Sandeep,

sure it can, if you take all the periodic replica of any atom into account (as 
one should).

SB

On Jun 30, 2011, at 7:28 PM, Sandeep Kumar wrote:

> Dear PWSCF users,
> I have carried out linear response phonon calculations for Al over a 4 * 4 * 
> 4 grid of q-points. This corresponds to a calculation in a supercell 
> comprised of 4 * 4* 4 unit cells (primitive).
> We recall that the lattice vectors in fractional coordinate system of a fcc 
> primitive cell are-
> a=(0.5, 0.5, 0.0)
> b=(0.0, 0.5, 0.5)
> c=(0.5, 0.0, 0.5)
> 
>> From the force-constant file (Al44.fc)  I obtained the force constant matrix 
>> Phi(i1,i2, na, nb) for pairs of atoms in the super-cell with the relative 
>> positions given  by
> R = (i-1)*a + (j-1)*b +(k-1)*c
> where i j and k are read from Al444.fc file.
> However, such a supercell does not include the pair of atoms located along 
> the cube axis direction i.e R = (a,0,0) or (0,a,0) or (0,0,a), and hence the 
> calculation CAN NOT give us the force-constant matrices along those pair of 
> atoms.
> How do we obtain the force-constant matrices for pair of atoms located along 
> the cube axes direction.
> I will be VERY VERY GRATEFUL to any help in this regard.
> 
> Sandeep K. Lahiri
> Department of Mechanical Engineering
> Massachusetts Institute of Technology
> Cambridge, MA
> ___
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---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni 
(skype)

La morale est une logique de l'action comme la logique est une morale de la 
pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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[Pw_forum] Query regarding real space interatomic force constant

[Sandeep Kumar]

Dear PWSCF users,
I have carried out linear response phonon calculations for Al over a 4 * 4 * 4 
grid of q-points. This corresponds to a calculation in a supercell comprised of 
4 * 4* 4 unit cells (primitive).
 We recall that the lattice vectors in fractional coordinate system of a fcc 
primitive cell are-
 a=(0.5, 0.5, 0.0)
 b=(0.0, 0.5, 0.5)
 c=(0.5, 0.0, 0.5)

[Pw_forum] Query regarding Al2O3 system slab calculation

[Ngoc Linh Nguyen]

Vikas Varshney wrote:
> Dear All,
>  
> My final motivation is to simulate adsorption of several small 
> molecules on Al2O3 slab. The strategy I am undertaking (and hence I 
> have few questions) is below. Please correct me if I am wrong at any 
> stage of my calculation.
>  
> I want to get the ground state of the Al2O3 slab. In this regard, I 
> got the unit cell of Al2O3 which is trigonal ( Space group R-3c, point 
> group D3d, 30 atoms) . This is not the primitive unit cell (which is 
> rhombhohedral and contain 10 atoms). The reason is to eventually 
> simulate 0 0 1 surface. It seems that the structure consist of 2 basis 
> atoms. The rest are defined by different symmetry operations for the 
> point group of Al2O3.
>  
> Is is possible to make use of symmetry operations and run the 
> calculation on unit cell of Al2O3 by specifying only two basis atoms 
> and then run slab calculation with 30 atoms? Or should I just create 
> a 30 atom unit cell with vacuum along Z direction in a slab geometry 
> and relax it? 
I am not clear about your question much.
Anyway, I do the simulation of adsorption on the slab by form a 
supercell that stores the substrate + vacuum + adsorbate atoms.
You can see in previous archives to understand how to form a supercell.

Best,

Linh

 






> Best Regards,
> Vikas
>  
>  
> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-
"The physics is theoretical but the fun is real"

[Pw_forum] Query regarding Al2O3 system slab calculation

[Vikas Varshney]

Dear All,

My final motivation is to simulate adsorption of several small molecules on
Al2O3 slab. The strategy I am undertaking (and hence I have few questions)
is below. Please correct me if I am wrong at any stage of my calculation.

I want to get the ground state of the Al2O3 slab. In this regard, I got the
unit cell of Al2O3 which is trigonal ( Space group R-3c, point group D3d, 30
atoms) . This is not the primitive unit cell (which is rhombhohedral and
contain 10 atoms). The reason is to eventually simulate 0 0 1 surface. It
seems that the structure consist of 2 basis atoms. The rest are defined by
different symmetry operations for the point group of Al2O3.

Is is possible to make use of symmetry operations and run the calculation on
unit cell of Al2O3 by specifying only two basis atoms and then run slab
calculation with 30 atoms? Or should I just create a 30 atom unit cell with
vacuum along Z direction in a slab geometry and relax it?

Best Regards,
Vikas
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[Pw_forum] Query about restarting vc-relax (Cesar R.S. da Silva)

[Cesar R.S. da Silva]

Dear Phillip,

I have used vc-relax for several years and never faced this problem.

Please, send me your input file and pseudo-potentials. I'll try to
reproduce your error, and fix it.

Cesar.






Cesar R.S. da Silva, PhD.
Minnesota Supercomputing Institute,
University of Minnesota.
Phone: (612)-624-7425   e-mail: cesards at msi.umn.edu

[Pw_forum] Query about restarting vc-relax

[Phillip English]

Dear users and developers,

 

I'm new to using PWscf, and I've been attempting to run some basic
calculations of TiO2 and its two predominant polymorphs, rutile and anatase.
I'm having no trouble running 'scf', 'relax', and 'vc-relax' calculations
for the rutile polymorph, as it finishes within one period of the time
allocated to me on our supercomputers. However, anatase takes a little bit
longer, so it is being cut off mid-calculation by the queueing system. From
what I understand, this is what the restart_mode='restart' flag is for, so I
have tried using that to restart my calculation.

 

Before I restarted the calculation, the energy was converging nicely towards
a value I expected. However as soon as I restarted, the energy blew out.
Looking at the cell parameters, they too blew out, and visualising the
structure showed that the cell was indeed expanding quite rapidly. When I
looked at the output more closely, it seemed like the starting cell
parameters for the restarted calculation were still being calculated by the
program according to the specified 'ibrav' and 'celldm' values, rather than
restarting with the cell parameters that had relaxed from the previous
calculation. This is what I supposed caused the 'explosion'. It seems
strange to me that while the atomic positions are read in correctly, the
cell parameters are not.

 

So, my question after that long preamble; do you need to manually re-enter
the cell parameters using the 'CELL_PARAMETERS' flag when restarting a
vc-relax calculation? If this isn't the case, does anyone have any ideas
about what might have caused the behaviour described.

 

Apologies if this has been covered before, I used the search function and a
google search on the mailing list archives to try and find the answer but
couldn't.

 

Cheers,

 

Phillip English

 

PhD Student

Curtin University, Perth

Western Australia

Australia

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[Pw_forum] Query about restarting vc-relax

[Paolo Giannozzi]

On Apr 17, 2008, at 13:48 , Phillip English wrote:

> However as soon as I restarted, the energy blew out. Looking at the  
> cell parameters, they too blew out, and visualising the structure  
> showed that the cell was indeed expanding quite rapidly. When I  
> looked at the output more closely, it seemed like the starting cell  
> parameters for the restarted calculation were still being  
> calculated by the program according to the specified ?ibrav? and  
> ?celldm? values, rather than restarting with the cell parameters  
> that had relaxed from the previous calculation. This is what I  
> supposed caused the ?explosion?. It seems strange to me that while  
> the atomic positions are read in correctly, the cell parameters are  
> not.
>

restarting from a variable-cell optimization / molecular dynamics  
run ? not
sure it works properly. If nobody has ever verified it, it is  
unlikely that it works.
The only parts of the distribution that typically work are either the  
most frequently
used, or those used by people willing to, and able to, improve the code.
> So, my question after that long preamble; do you need to manually  
> re-enter the cell parameters using the ?CELL_PARAMETERS? flag when  
> restarting a vc-relax calculation?
>
not unlikely, but it might not be sufficient

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] Query about restarting vc-relax

[Axel Kohlmeyer]

On Thu, 17 Apr 2008, Phillip English wrote:

PE> Dear users and developers,
PE> 
PE>  
PE> 
PE> I'm new to using PWscf, and I've been attempting to run some basic
PE> calculations of TiO2 and its two predominant polymorphs, rutile and anatase.
PE> I'm having no trouble running 'scf', 'relax', and 'vc-relax' calculations
PE> for the rutile polymorph, as it finishes within one period of the time
PE> allocated to me on our supercomputers. However, anatase takes a little bit
PE> longer, so it is being cut off mid-calculation by the queueing system. From

phillip,

please consider setting the 'max_seconds' flag to a value
of, say, 15 mins less than the maximum run time of your
batch job. this way you make sure that the job stops cleanly
and is thus cleanly restartable. i don't know whether this will
solve your problem, but it might cure future problems when
you jobs get randomly killed in the middle of writing a restart
for example.

cheers,
axel.

p.s.: if this is a real bug, it would be nice to know which
OS/compiler/QE-version this relates to. perhaps it has been
found and fixed already in the cvs version?

PE> what I understand, this is what the restart_mode='restart' flag is for, so I
PE> have tried using that to restart my calculation.
PE> 

-- 
===
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
===
If you make something idiot-proof, the universe creates a better idiot.