[Pw_forum] Not able to run after restarting electron minimization

[shashi bhusan mishra]

Dear QE users,

I want to run cp.x for long time (nearly 20-30ps) for a heavy
system like LiFePO4. Starting form the minimized structure (after electron
minimization & randomization) I checked the dynamics run in microcanonical
ensemble which runs very fine (total constant of motion nearly constant
asthe criteria suggests). But when I run the simulation using Nose-hoover
thermostat for 10-20 ps the electron fictitious kinetic energy increases
rapidly which suggests that the system is not proceeding in the right
direction. As suggested I minimized the electron ke  again and restated the
simulation using NH thermostat. But results after re minimization is not
proceeding in the correct way. So, help me how to restart the dynamics for
long time step.

&control
calculation = 'cp'
nstep  = 5,
iprint = 10,   isave  = 100,
dt= 4.0d0,
etot_conv_thr = 1.d-9,   ekin_conv_thr = 1.d-5,
 /
 &system
nat=  55,  ntyp= 8,
ecutwfc =30.0, ecutrho = 250.0,
nr1b=12,nr2b=12,nr3b=12,
 /
 &electrons
emass = 400.d0, emass_cutoff = 2.5d0,
orthogonalization = 'ortho',
ortho_eps = 5.d-8, ortho_max = 20,
electron_dynamics = 'verlet',
!electron_damping = 0.1,
electron_velocities ='zero'
 /
 &ions
ion_dynamics ='verlet',
ion_velocities='zero', ion_temperature = 'nose', fnosep = 24., tempw=
2000.
 /
 &cell
cell_dynamics = 'none', press = 0.0d0,

Any help would be appreciated.

Shashi Bhusan Mishra
Research Scholar,
Dept. Of Physics,
Room No- HSB209A
IIT Madras-36
9087218085
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[Pw_forum] vc-relax_ERROR

[Mofrad, Amir Mehdi (MU-Student)]

Dear all QE users and developers,

I want to do a "vc-relax" calculation, however I get the following error:

task # 0
 from scale_h : error # 1
 Not enough space allocated for radial FFT: try restarting with a larger 
cell_factor.


And here is also my input file:

 &CONTROL
 calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
  wf_collect = .true. ,
  outdir = './scratch' ,
  wfcdir = './scratch' ,
  pseudo_dir = '/global/espresso/pseudo' ,
  prefix = 'SOD' ,
   verbosity = 'high' ,
   etot_conv_thr = 1e-5 ,
   forc_conv_thr = 1e-4 ,
   nstep = 50 ,
 tstress = .true. ,
 tprnfor = .true. ,
 /
 &SYSTEM
   ibrav = 0,
 nat = 36,
ntyp = 2,
 ecutwfc = 15 ,
 ecutrho = 150 ,
 /
 &ELECTRONS
electron_maxstep = 100,
conv_thr = 3e-8 ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.7 ,
 diagonalization = 'david' ,
 /
 &IONS
ion_dynamics = 'bfgs' ,
trust_radius_ini = 0.5 ,
 /
&CELL
cell_dynamics = 'bfgs',
/
CELL_PARAMETERS bohr
16.7202967500.00.0
 0.0   16.7202967500.0
 0.00.0   16.720296750
ATOMIC_SPECIES
   Si   28.08600  Si.pbe-n-rrkjus_psl.0.1.UPF
O   15.99940  O.pbe-n-rrkjus_psl.0.1.UPF
 ATOMIC_POSITIONS angstrom
   Si  2.212000.04.42400
   Si  6.636000.04.42400
   Si  4.424002.212000.0
   Si  4.424006.636000.0
   Si  0.04.424002.21200
   Si  0.04.424006.63600
   Si  2.212004.424000.0
   Si  6.636004.424000.0
   Si  0.02.212004.42400
   Si  0.06.636004.42400
   Si  4.424000.02.21200
   Si  4.424000.06.63600
O  1.208643.838261.31835
O  7.639365.009741.31835
O  7.639363.838267.52965
O  1.208645.009747.52965
O  1.318351.208643.83826
O  1.318357.639365.00974
O  7.529657.639363.83826
O  7.529651.208645.00974
O  3.838261.318351.20864
O  5.009741.318357.63936
O  3.838267.529657.63936
O  5.009747.529651.20864
O  8.262265.632645.74235
O  0.585743.215365.74235
O  8.262263.215363.10565
O  0.585745.632643.10565
O  5.632645.742358.26226
O  3.215365.742350.58574
O  3.215363.105658.26226
O  5.632643.105650.58574
O  5.742358.262265.63264
O  5.742350.585743.21536
O  3.105658.262263.21536
O  3.105650.585745.63264
K_POINTS automatic
  4 4 4   1 1 1


Any help would be appreciated.


Amir M. Mofrad

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Re: [Pw_forum] Restart_A_Job

[Mofrad, Amir Mehdi (MU-Student)]

Thank You Josh for your help.



Amir M. Mofrad

Graduate Research Assistant

Chemical Engineering Department

University of Missouri



From: pw_forum-boun...@pwscf.org  on behalf of 
Joshua Davis 
Sent: Tuesday, February 16, 2016 4:25 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Restart_A_Job

Dear Mofrad

You can probably use the 
max_seconds
 value under &CONTROL and use a different 
disk_io
 option if you are really worried about your job not exiting at the proper time.


Joshua D. Davis

Graduate Assistant
Department of Chemistry
Michigan State University

-

On Tue, Feb 16, 2016 at 4:19 PM, Mofrad, Amir Mehdi (MU-Student) 
mailto:am...@mail.missouri.edu>> wrote:

Dear all QE users and developers,


I have been running my calculations on a cluster which does not allow me to use 
the resources on cluster more than two days. I was wondering if there is a way 
to stop my job clean (before it exceeds two days) and then restart it from 
where it was stopped so that I don't lose my job and still can continue my job.



Best,



Amir M. Mofrad

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Re: [Pw_forum] Restart_A_Job

[Joshua Davis]

Dear Mofrad

You can probably use the max_seconds

value
under &CONTROL and use a different disk_io

option
if you are really worried about your job not exiting at the proper time.


Joshua D. Davis

Graduate Assistant
Department of Chemistry
Michigan State University

-

On Tue, Feb 16, 2016 at 4:19 PM, Mofrad, Amir Mehdi (MU-Student) <
am...@mail.missouri.edu> wrote:

> Dear all QE users and developers,
>
>
> I have been running my calculations on a cluster which does not allow me
> to use the resources on cluster more than two days. I was wondering if
> there is a way to stop my job clean (before it exceeds two days) and then
> restart it from where it was stopped so that I don't lose my job and still
> can continue my job.
>
>
>
> Best,
>
>
>
> Amir M. Mofrad
>
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[Pw_forum] Restart_A_Job

[Mofrad, Amir Mehdi (MU-Student)]

Dear all QE users and developers,


I have been running my calculations on a cluster which does not allow me to use 
the resources on cluster more than two days. I was wondering if there is a way 
to stop my job clean (before it exceeds two days) and then restart it from 
where it was stopped so that I don't lose my job and still can continue my job.



Best,



Amir M. Mofrad
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Re: [Pw_forum] External Magnetic field

[Arles V. Gil Rebaza]

Hi Pulkit, try with Wien2K code (http://www.wien2k.at/) or ELK code (
http://elk.sourceforge.net/) , the last one is free, and both codes are
based on the LAPW framework.

Best

Arles V. Gil Rebaza
Instituto de Física La Plata
La Plata -  Argentina


2016-02-16 14:21 GMT-03:00 Pulkit Garg :

> Hi all,
>
> I want to apply an external Magnetic field on my material. Can I do that
> in QE, if yes then how? If no then is there any software or package that
> allows me to do that?
>
> Thanks,
>
> Pulkit Garg
>
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-- 
###->   Arles V.   <-###
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[Pw_forum] Structural Optimization Calculation

[Cameron Foss]

Hello all,

I am trying to run a relaxation calculation on a monolayer of a transition
metal dichalcogenide of Molydenum Diselenide (MoSe2) to then further obtain
vibrational modes of that monolayer. I am using QE-5.1 with LDA
functionals. I want the monolayer material so vdW corrections are neglected
in this case. I am somewhat confident in the in-plane lattice constant but
I am trying to relax the Se-Se distance to the equilibrium structure. Below
is the input file for the relaxation:

&control
calculation='relax'
restart_mode='from_scratch',
!pseudo_dir='directory where pseudopotentials are stored/',
!outdir='directory where large files are written/'
pseudo_dir='/home/cjfoss/espresso-5.1/pseudo/',
outdir='/home/cjfoss/espresso-5.1/2dout'
prefix='mose2PH_v7',
 /
 &system
ibrav=4, celldm(1)=6.2134195, celldm(3)=8,
nat=3, ntyp=2, ecutwfc =140
 /
 &electrons
conv_thr =  1.0d-14
mixing_beta = 0.7
 /
&ions
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
 Mo  95.94Mo.pw-mt_fhi.UPF
 Se  78.96Se.pw-mt_fhi.UPF
ATOMIC_POSITIONS alat
Se   0.0   0.0   3.0 1 1 1
Mo   0.5   0.288675135   3.493465193 1 1 1
Se   0.0   0.0   3.986930347 1 1 1
K_POINTS automatic
 6 6 4 1 1 1

I expect this simulation to allow the *atomic positions* to relax leaving
the actual lattice constant unchanged. I also expect the atomic positions
to relax in all 3 directions (hence the 1 1 1 after each coordinate
specification) but I have seen the x and y coordinates remain relatively
unchanged. Again I am really after the Se-Se distance.

My questions are: is this relaxation calculation doing what I expect it to
do? And is the equilibrium structure guaranteed if convergence is achieved?
The motivation for the second question is that, I have run a relaxation
calculation with this input file, it converges, but then I find negative
frequencies in the phonon dispersion particularly with the ZA and TA modes
(the ZA mode being the characteristic quadratic mode found in 2D monolayers
such as graphene and would be most susceptible to variations in the Se-Se
distance). As the simulation experienced no interruptions I suspect the
negative frequencies to be a result of numerical issues with the atomic
positions and/or the MP grid size (note I used an 8 8 1 grid size for the
phonon calculation, not 6 6 4 as mentioned above)

A third question: Is there perhaps a better way to perform a relaxation
calculation? or am I oversimplifying the system -- that is MoSe2 consists
of a transition metal (Mo) and 2 chalcogens (Se), are there additional
parameters that should be stated that I am leaving out?

Best regards,
Cameron
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[Pw_forum] External Magnetic field

[Pulkit Garg]

Hi all,

I want to apply an external Magnetic field on my material. Can I do that in
QE, if yes then how? If no then is there any software or package that
allows me to do that?

Thanks,

Pulkit Garg
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Re: [Pw_forum] Volume Optimisation :-Reg

[Ari P Seitsonen]

Dear A Suresh,

  My standard answer, sorry for that - did you check that the value of 
'ecutwfc' is sufficient? In the Good Old Days (at FHI) we used to use 
something more like 80-100 Ry for FHI-pseudos of oxygen, and that in 
ionc relaxations-only: The 'vc-relax' requires yet-a higher value. Did you 
try to start a new calculation from the lattice+ionic geometry that you 
obtained, _without_ restarting the electronic structure (ie copying the 
new values lattice vectors and ionic coordinates into the input file and 
keeping the "restart_mode = 'from_scratch'"): If the lattice constants 
start to change a lot, the cut-off energy is too low. Or you look at the 
value of the stress at the end of your previous calculation: The final 
step is done with re-generated plane waves, so if your lattice changed a 
lot and the cut-off was too low, there suddenly is a large value of 
stress.


  On the other hand I do not know about the accuracy of the pseudo 
potential for Ti: I remember there were some problems with a 
norm-conserving one, at least if the number of valence electrons is four. 
Maybe this one would work better, I do not know this one, but I would 
start checking the value of the cut-off energy.


Greetings from Sunny Paris,

   apsi

PS Why this "exxdiv_treatment" in your input...?

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 16 Feb 2016, Suresh A wrote:


Dear All,
    I have optimized the structure for anatase simple tetragonal. The 
optimiized lattice parameters are a= 3.754336A. c=9.193631522694A. but the 
experimental values are
a= 3.785A, c=9.514A. There is big difference in c value for optimised 
strucutre.But the same calculation for GGA pseudo potential gives the lattice 
parameter values which are
good with  experimental values. In literature  previous results for LDA has 
good lattice parameter values.
 Which parameter I have to  change in order to get good results for LDA?
  Below is my input and the version i have used is 5.2.1

 &CONTROL
   title = 'anatase' ,
 calculation = 'vc-relax' ,
    restart_mode = 'from_scratch' ,
  pseudo_dir = '/home/suresh/GN2/',
  outdir ='/home/suresh/Desktop/ashahicheck/asahiopt/tmp/',
  prefix = 'anatase' ,
 tstress = .true. ,
 tprnfor = .true. ,
 /
 &SYSTEM
   ibrav = 6,
   A = 3.692,
   C = 9.471 ,
 nat = 12,
    ntyp = 2,
 ecutwfc = 60 ,
    exxdiv_treatment = 'none' ,
 /
 &ELECTRONS
 /
 &IONS
  ion_dynamics = 'bfgs' ,
 /
 &CELL
   cell_dynamics = 'bfgs' ,
 /
ATOMIC_SPECIES
   Ti   47.86700  Ti.pz-mt_fhi.UPF
    O   15.99940  O.pz-mt_fhi.UPF
ATOMIC_POSITIONS (crystal)
Ti  0.000   0.000   0.000
Ti  0.500   0.000   0.750
Ti  0.000   0.500   0.250
Ti  0.500   0.500   0.500
O   0.000   0.000   0.2066000
O   0.500   0.000   0.5434000
O   0.000   0.500   0.4566000
O   0.500   0.000   0.9566000
O   0.000   0.500   0.0434000
O   0.000   0.000   0.7934000
O   0.500   0.500   0.7066000
O   0.500   0.500   0.2934000
K_POINTS automatic
4 4 2 1 1 1


Thanks in advance.


  With Regards,
A.Suresh,
Research Scholar,
Madurai Kamaraj University,
Madurai.

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Re: [Pw_forum] Effective mass calculator

[ulrich.aschauer]

Dear Fataneh,

When I did this a while ago I found it easiest to let emc.py generate the 
stencil grid and copy the relevant part of the KPOINTS file into a pw.x nscf 
file. After running the nscf you can extract the eigenvalues back into an 
EIGENVAL formatted file for analysis by emc.py. This last step can be done with 
the attached script.

Not the most direct and elegant way, but it worked.

Best regards,
-uli

--
SNF Prof. Dr. Ulrich Aschauer
Universität Bern
Departement für Chemie und Biochemie
Freiestrasse 3
CH-3012 Bern
Tel. +41 (0)31 631 5629
ulrich.ascha...@dcb.unibe.ch
www.dcb.unibe.ch
Büro: N431
--


On 16 Feb 2016, at 09:00, fataneh bostan afroz 
mailto:fbostanaf...@gmail.com>> wrote:

Dear
I want to calculate Effective mass using quantum espresso.
 Is it possible to calculate effective mass using  Effective mass calculator ( 
EMC) in quantum espresso such as  are implemented for Vasp and CRYSTAL in this 
link
http://afonari.com/emc/?

pleas giud me.
thank you
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pw_nscf_2_EIGENVAL.sh.tar.gz
Description: pw_nscf_2_EIGENVAL.sh.tar.gz
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[Pw_forum] Effective mass calculator

[fataneh bostan afroz]

Dear
I want to calculate Effective mass using quantum espresso.
* Is it possible to calculate effective mass using * Effective mass
calculator ( EMC)* in quantum espresso such as  are **implemented for Vasp
and CRYSTAL in this link*

*http://afonari.com/emc/ ?*

*pleas giud me.*
*thank you*
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