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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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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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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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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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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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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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:
> >
> > &control
> > 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/'
> >  /
> >  &system
> > 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
> >  /
> >  &electrons
> > 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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> > 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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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.
>
> &control
> 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
>  /
>  &system
>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.
>  /
>  &electrons
> diagonalization='david'
> mixing_mode = 'plain'
> mixing_beta = 0.1
> conv_thr =  1.0d-5
> electron_maxstep=200
>  /
> &ions
> /
> &cell
> 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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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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