Re: [Pw_forum] vc-relax + vdW-DF2. PWSCF v.6.1

2017-10-31 Thread Ronald Cohen 
In 6.2 compiled with -DSPIN_BALANCED  rvv10 seems to work fine with DFT+U but 
DF2 with spin_balanced gives stresses that do not converge. The error is not 
large but finite:
df2 dft+u
 total   stress  (Ry/bohr**3)   (kbar) P=   24.12
  total   stress  (Ry/bohr**3)   (kbar) P=   24.96
  total   stress  (Ry/bohr**3)   (kbar) P=   25.25
  total   stress  (Ry/bohr**3)   (kbar) P=   25.47
  total   stress  (Ry/bohr**3)   (kbar) P=   25.80
  total   stress  (Ry/bohr**3)   (kbar) P=   25.41
  total   stress  (Ry/bohr**3)   (kbar) P=   25.43
  total   stress  (Ry/bohr**3)   (kbar) P=   25.30
  total   stress  (Ry/bohr**3)   (kbar) P=   25.28
  total   stress  (Ry/bohr**3)   (kbar) P=   25.13
  total   stress  (Ry/bohr**3)   (kbar) P=   25.33
  total   stress  (Ry/bohr**3)   (kbar) P=   25.44
  total   stress  (Ry/bohr**3)   (kbar) P=   25.49
rvv10 (same system and setup) converges fine (still running):
  total   stress  (Ry/bohr**3)   (kbar) P=  105.54
  total   stress  (Ry/bohr**3)   (kbar) P=  -36.11
  total   stress  (Ry/bohr**3)   (kbar) P=  -37.82
  total   stress  (Ry/bohr**3)   (kbar) P=5.90
  total   stress  (Ry/bohr**3)   (kbar) P=   -2.78
  total   stress  (Ry/bohr**3)   (kbar) P=   -8.11
  total   stress  (Ry/bohr**3)   (kbar) P=   -5.48
  total   stress  (Ry/bohr**3)   (kbar) P=   -1.83

---
Ronald Cohen
Extreme Materials Initiative
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rco...@carnegiescience.edu 
office: 202-478-8937
skype: ronaldcohen

> On 27 Oct 2017, at 15:10, Paolo Giannozzi  wrote:
> 
> Please delete Modules/xc_vdW_DF.o and PW/src/stres_nonloc_dft.o, recompile 
> with -D__SPIN_BALANCED
> 
> Paolo
> 
> On Fri, Oct 27, 2017 at 1:34 PM, Ronald Cohen  > wrote:
> I still get:
>  
> %%
>  Error in routine stres_vdW_DF (1):
>  vdW stress not implemented for nspin > 1
>  
> %%
> 
>  stopping ...
>  Performing spin-balanced Ecnl stress calculation!
> 
> %%
>  Error in routine stres_vdW_DF (1):
>  vdW stress not implemented for nspin > 1
>  
> %%
> 
>  stopping ...
> ---
> Ronald Cohen
> Extreme Materials Initiative
> Geophysical Laboratory
> Carnegie Institution
> 5251 Broad Branch Rd., N.W. 
> 
> Washington, D.C. 20015 
> 
> rco...@carnegiescience.edu 
> office: 202-478-8937 
> skype: ronaldcohen
> 
>> On 27 Oct 2017, at 07:14, Prof. Dr. Ronald Cohen > > wrote:
>> 
>> Hi! I compiled qe 6.2 with -D__SPIN_BALANCE but I still get:
>> from stres_vdW_DF : error # 1
>>  vdW stress not implemented for nspin > 1
>> Should I just take out that error in the code and let it try to run?
>> 
>> Attached is my input and output.  Thanks!
>> 
>> Ron
>> 
>> ---
>> Professor Dr. Ronald Cohen
>> Ludwig Maximilians Universität
>> Theresienstrasse 41 Room 
>> 
>>  207 
>> 
>> Department für Geo- und Umweltwissenschaften
>> München
>> 80333
>> Deutschland
>> 
>> office: +49 089 2180 4294 
>> ronald.co...@min.uni-muenchen.de 
>> skypename: ronaldcohen
>> 
>> 
>>> On 24 Oct 2017, at 11:27, Bogdan Yavorskyy 
>>> >> > wrote:
>>> 
>>> 
>>> 
 Begin forwarded message:
 
 From: Paolo Giannozzi >>> >
 Subject: Re: [Pw_forum] vc-relax + vdW-DF2. PWSCF v.6.1
 Date: 24 October 2017 at 17:24:41 CEST
 To: PWSCF Forum mailto:pw_forum@pwscf.org>>
 Cc: bogdan.yavors...@lrz.uni-muenchen.de 
 
 
 In the 6.2 version, it is possible to use the "spin-balanced" approach, 
 setting the -D__SPIN_B

Re: [Pw_forum] Fwd: Error in final scf calculation using vc-relax

2017-10-31 Thread Malte Sachs 

Dear Paolo,

thank you very much for your fast reply. Your patch works fine!

Best regards,
Malte

Am 30.10.2017 um 17:38 schrieb Paolo Giannozzi:
On Mon, Oct 30, 2017 at 1:11 PM, Malte Sachs 
> wrote:


[...] in version 6.1/6.2 I get:

/ Starting magnetic structure//
// atomic species   magnetization//
//    U  NaN/

Uranium is poisonous for people, Sodium Nitride for computer codes

[...] the structure doesn't contain Uranium atoms


Maybe I know what is happening and why: try first to run the same 
input without U (that is: ntyp=1, no line with U PP). If it works, 
apply the following patch, try again with U. A change done just before 
v.6.1 wasn't checking for a case like yours (no atoms of a given type)


Index: PW/src/move_ions.f90
===
--- PW/src/move_ions.f90    (revision 13970)
+++ PW/src/move_ions.f90    (working copy)
@@ -474,9 +474,11 @@
    END IF
 END IF
  END DO
- starting_magnetization(i) = starting_magnetization(i) / REAL(nt)
- angle1(i) = angle1(i) / REAL(nt)
- angle2(i) = angle2(i) / REAL(nt)
+ IF ( nt > 0 ) THEN
+    starting_magnetization(i) = starting_magnetization(i) / DBLE(nt)
+    angle1(i) = angle1(i) / DBLE(nt)
+    angle2(i) = angle2(i) / DBLE(nt)
+ END IF
   END DO
   DEALLOCATE ( r_loc, m_loc )

--
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



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum



--
Malte Sachs
Anorganische Chemie, Fluorchemie
Philipps-Universität Marburg
Hans-Meerwein-Straße 4
35032 Marburg (Paketpost: 35043 Marburg)
Tel.: +49 (0)6421 28 - 25 39 5
http://www.uni-marburg.de/fb15/ag-kraus/



smime.p7s
Description: S/MIME Cryptographic Signature
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] solve_linter: root not converged in Phonon Calculation

2017-10-31 Thread yuan liang 
Dear QE users,

I am a beginner in QE and am performing some calculation on phonons of
YVO3 in order to get the phonon dos

I ran SCF first and then did PH.x at a grid of 3*3*2 with 8
irreducible q-vectors.

However in ph.x output file of this specific q-point(0.0,
0.315030085373153, -0.349748181309457E),

I got this error message on mode #12:

*Representation # 12 mode #  12

 Self-consistent Calculation
 kpoint   1 ibnd  87 solve_linter: root not convergedNaN
 kpoint   2 ibnd  88 solve_linter: root not convergedNaN
 kpoint   3 ibnd  89 solve_linter: root not convergedNaN
 kpoint   4 ibnd  87 solve_linter: root not convergedNaN
 kpoint   5 ibnd  88 solve_linter: root not convergedNaN
 kpoint   6 ibnd  89 solve_linter: root not convergedNaN
 kpoint   7 ibnd  89 solve_linter: root not convergedNaN
 kpoint   8 ibnd  89 solve_linter: root not convergedNaN
 kpoint   9 ibnd  89 solve_linter: root not convergedNaN
 kpoint  10 ibnd  89 solve_linter: root not convergedNaN
 kpoint  11 ibnd  91 solve_linter: root not convergedNaN
 kpoint  12 ibnd  93 solve_linter: root not convergedNaN
 kpoint  13 ibnd  87 solve_linter: root not convergedNaN
 kpoint  14 ibnd  88 solve_linter: root not convergedNaN
 kpoint  15 ibnd  87 solve_linter: root not convergedNaN
 kpoint  16 ibnd  88 solve_linter: root not convergedNaN
 kpoint  17 ibnd  88 solve_linter: root not convergedNaN
 kpoint  18 ibnd  89 solve_linter: root not convergedNaN
 kpoint  19 ibnd  88 solve_linter: root not convergedNaN
 kpoint  20 ibnd  88 solve_linter: root not convergedNaN
 kpoint  21 ibnd  89 solve_linter: root not convergedNaN
 kpoint  22 ibnd  89 solve_linter: root not convergedNaN
 kpoint  23 ibnd  89 solve_linter: root not convergedNaN
 kpoint  24 ibnd  89 solve_linter: root not convergedNaN
 kpoint  25 ibnd  88 solve_linter: root not convergedNaN
 kpoint  26 ibnd  88 solve_linter: root not convergedNaN
 kpoint  27 ibnd  89 solve_linter: root not convergedNaN
 kpoint  28 ibnd  89 solve_linter: root not convergedNaN
 kpoint  29 ibnd  89 solve_linter: root not convergedNaN
 kpoint  30 ibnd  89 solve_linter: root not convergedNaN
 kpoint  31 ibnd  89 solve_linter: root not convergedNaN
 kpoint  32 ibnd  89 solve_linter: root not convergedNaN
 kpoint  33 ibnd  89 solve_linter: root not convergedNaN
 kpoint  34 ibnd  89 solve_linter: root not convergedNaN
 kpoint  35 ibnd  89 solve_linter: root not convergedNaN
 kpoint  36 ibnd  89 solve_linter: root not convergedNaN
 kpoint  37 ibnd  89 solve_linter: root not convergedNaN
 kpoint  38 ibnd  89 solve_linter: root not convergedNaN
 kpoint  39 ibnd  93 solve_linter: root not convergedNaN
 kpoint  40 ibnd  91 solve_linter: root not convergedNaN
 kpoint  41 ibnd  89 solve_linter: root not convergedNaN
 kpoint  42 ibnd  91 solve_linter: root not convergedNaN
 kpoint  43 ibnd  89 solve_linter: root not convergedNaN
 kpoint  44 ibnd  89 solve_linter: root not convergedNaN
 kpoint  45 ibnd  89 solve_linter: root not convergedNaN
 kpoint  46 ibnd  89 solve_linter: root not convergedNaN
 kpoint  47 ibnd  89 solve_linter: root not convergedNaN
 kpoint  48 ibnd  89 solve_linter: root not convergedNaN
 kpoint  49 ibnd  87 solve_linter: root not convergedNaN
 kpoint  50 ibnd  88 solve_linter: root not convergedNaN
 kpoint  51 ibnd  89 solve_linter: root not convergedNaN
 kpoint  52 ibnd  89 solve_linter: root not convergedNaN
 kpoint  53 ibnd  89 solve_linter: root not convergedNaN
 kpoint  54 ibnd  89 solve_linter: root not convergedNaN
 kpoint  55 ibnd  88 solve_linter: root not convergedNaN
 kpoint  56 ibnd  88 solve_linter: root not convergedNaN
 kpoint  57 ibnd  89 solve_linter: root not convergedNaN
 kpoint  58 ibnd  88 solve_linter: root not convergedNaN
 kpoint  59 ibnd  88 solve_linter: root not convergedNaN
 kpoint  60 ibnd  89 solve_linter: root not convergedNaN
 kpoint  61 ibnd  89 solve_linter: root not convergedNaN
 kpoint  62 ibnd  89 solve_linter: root not convergedNaN
 kpoint  63 ibnd  89 solve_linter: root not convergedNaN
 kpoint  64 ibnd  89 solve_linter: root not convergedNaN
 kpoint  65 ibnd  89 solve_linter: root not convergedNaN
 kpoint  66 ibnd  89 solve_linter: root not convergedNaN
 kpoint  67 ibnd  91 solve_l

Re: [Pw_forum] Relax - Killed

2017-10-31 Thread Giuseppe Mattioli 

Dear Nkosinathi Malaza (please sign always your posts with name and  
scientific affiliation)

It is very likely that your calculation crashed because you ran out of  
RAM. I can't say more without seeing your input file. In recent QE  
versions there is a rough estimate of the memory requirements of pw.x  
calculations. You find it before the first scf step, something like  
this:

   Estimated max dynamical RAM per process > 252.38MB

  Estimated total allocated dynamical RAM >9085.67MB

In my experience it is usually a bit on the side of overestimation. If  
your machine has more RAM than this your calculation should not crash  
because of memory shortage.

HTH
Giuseppe

Quoting Nkosinathi Malaza :

> Dear users,
>
> I've tried to relax a system of about 350 atoms on a computer with 96G of
> RAM, the calculation does not run I get the error below. I've tried to
> lower the number of k-points, but still I get the same error. Please assist
> with this problem.
>
>   total cpu time spent up to now is 1297.7 secs
>
> Self-consistent Calculation
>
> iteration #  1 ecut=70.00 Ry beta=0.30
> Davidson diagonalization with overlap
> --
> mpirun noticed that process rank 4 with PID 36487 on node avx1-1 exited on
> signal 9 (Killed).
> --
>
>
>
> Thank you



GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] How to calculate Mean Square Displacement (MSD)

2017-10-31 Thread Vahid Askarpour 
Dear Nam,

My understanding is that the trajectory as printed in VASP’s XDATCAR is folded 
or wrapped. As you can see in msd.f90,:

write(6,*) 'Name of unwrapped xyz file’

So the input file should be unwrapped. In other words, you have to first unwrap 
the coordinates in XDATCAR. Then you can use msd.f90.

To unwrap the coordinates, there are other codes on that website such as 
unwrap_PBC.f90.

Cheers,

Vahid


On Oct 30, 2017, at 9:25 PM, Nam Tran 
mailto:vnt...@uowmail.edu.au>> wrote:

Dear Vahid

I don't know whether VASP folds back atoms in their output or not. If they do 
then the msd.f90 you recommended is not accurate. Because the code simply 
calculate the distance between two position

dRx = Rx(j) - Rx0(j)
dRy = Ry(j) - Ry0(j)
dRz = Rz(j) - Rz0(j)
sum_msd = sum_msd + (dRx**2 + dRy**2 + dRz**2)

One thing is that I tried to create a .axsf file using cppx. And the atoms seem 
to be not folded back. Can someone confirm me that?

Best Regards,
Nam Tran



From: pw_forum-boun...@pwscf.org 
mailto:pw_forum-boun...@pwscf.org>> on behalf of 
Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Monday, October 30, 2017 11:00:01 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] How to calculate Mean Square Displacement (MSD)

There is a collection of fortran codes (for VASP mainly but can easily be 
adapted) for processing simulation output including MSD calculation and the 
treatment of periodic images. They can be found at https://github.com/boates 
under the Physics repository (see msd.f90).

Cheers,

Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University,
Halifax, NS, Canada


On Oct 30, 2017, at 4:29 AM, Nam Tran 
mailto:vnt...@uowmail.edu.au>> wrote:

Dear QE experts,

I am trying to evaluate MSD for my simulation.
My problem is that when an atom exits the simulation cell.
I do not know whether I should consider the distance with atom that goes about 
outside the box (a) or its image (b). Please check the image below (Blue is the 
original position t=0, red is the position at time t)


Best Regards
Nam Tran
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Phonon frequencies could not converge of ENCUT by version 5.2.

2017-10-31 Thread 黄志硕 
Dear all users,


I encountered one problem when doing consistency test of parameters of
phonon frequencies at Gamma point, shown as in the Table below, in which
are the lowest phonon frequencies of Gamma point after applying ASR.


>From the table, we can see that for smearing (S (Ry)), the frequency
converge well except smearing=0.125Ry, which is understandable because of
the too large value of smearing.  The problem part is the convergence of
ENCUT. In general, the larger ENCUT is, the better results are. But for
higher ENCUT, it does not converge. Could anyone give me any instructions
why the convergent of ENCUT is like this, I will appreciate it.


The K-mesh is 4*4*4 which turns out OK for the system and all of structures
are well relaxed under the parameters. And the calculations are carried out
by Quantum Espresso-5.2.



ENCUT/(Ry)
40 45 50 55 60 65 70
S
(Ry) 0.005 -67.2 -0.37 -0.37 -127.84 -0.28 -0.25 -87.94
0.010 -66.91 -0.37 -0.37 -127.88 -0.26 -0.25 -87.88
0.025 -67.57 -0.35 -0.38 -127.69 -0.31 -0.26 -87.93
0.125 -- -2196.53  -2273.29  -22497.9  -2203.83  -3215.92  -2258.14​

The input file of the scf calculation is shown below:

 &control
calculation='scf'
restart_mode='from_scratch',
prefix='K3C60',
pseudo_dir = './',
outdir='./',
tstress = .true.
tprnfor = .true.
 /
 &system
ibrav= 2, celldm(1)= 26.9097, nat=63, ntyp=2, nbnd=137
ecutwfc = 70, ecutrho = 280
occupations='smearing', smearing='gaussian', degauss=0.005
 /
 &electrons
mixing_beta = 0.7, conv_thr = 1.0D-10
 /
 &ions
ion_dynamics = 'damp'
 /
ATOMIC_SPECIES
 C  12  C.pbe-mt.UPF
 K  39.1  K.pbe-mt_norel.UPF
ATOMIC_POSITIONS (angstrom)
C1.167584737   3.033367455   1.424268580
C0.721014984   2.305670430   2.591830404
C   -0.721014984   2.305670430   2.591830404
.
.
.
K_POINTS automatic
4 4 4 1 1 1

With the phonon calculation input file:

Phonon of K3C60
 &inputph
  tr2_ph=1.0d-17,
  prefix='K3C60',
  recover=.true.
  amass(1)=12
  amass(2)=39.1
  outdir='./',
  fildyn='K3C60.dynG',
 /
0.0 0.0 0.0


Best regards

Zhishuo Huang
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Phonon calulcation with nonlocal vdW correction by version 6.2. 'Error in routine openfilq (1): file **.wfc not found'

2017-10-31 Thread 黄志硕 
Dear Quantum Espresso users,

Recently I used the latest version of quantum espresso (6.2) to calculate
the phonon dispersion with nonlocal vdW correction by setting the tag
input_dft='vdW-DF'. And I used the splitting mode for the calculation.

However, the calculation of 'start_q=1, last_q=1' in the splitting
calculation worked properly, while others ran into an error shown below:

###
 Error in routine openfilq (1):
 file **.wfc not found
###

I will be appreciated if anyone could give me any instructions.

Best regards
Zhishuo Huang
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Phonon calulcation with nonlocal vdW correction by version 6.2. 'Error in routine openfilq (1): file **.wfc not found'

2017-10-31 Thread 黄志硕 
Dear Quantum Espresso users,

Recently I used the latest version of quantum espresso (6.2) to calculate
the phonon dispersion with nonlocal vdW correction by setting the tag
input_dft='vdW-DF'. And I used the splitting mode for the calculation.

However, the calculation of 'start_q=1, last_q=1' in the splitting
calculation worked properly, while others ran into an error shown below:

###
 Error in routine openfilq (1):
 file **.wfc not found
###

I will be appreciated if anyone could give me any instructions.

Best regards
Zhishuo Huang
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum