[Pw_forum] QE-5.1.2: NEB.X Crashes with MPI errors

[Mauro Sgroi]

Dear All,
I'm trying to submit a NEB calculation on the Mn3/4Co1/4PO4 system to
calculate the Lithium energy barrier for diffusion. The baseline
calculation on MnPO4 went fine.
Inserting the cobalt atoms neb.x crashes during the calculation on the
second image.
No error is printed in the log but in the standard output I obtain:

  2   2 INTERMEDIATE_IMAGE
[t12node084:17231] 55 more processes have sent help message
help-mpi-btl-openib.txt / reg mem limit low
[t12node084:17231] Set MCA parameter "orte_base_help_aggregate" to 0 to see
all help / error messages
[t12node082:28692] *** An error occurred in MPI_Bcast
[t12node082:28692] *** on communicator MPI COMMUNICATOR 9 SPLIT FROM 7
[t12node082:28692] *** MPI_ERR_TRUNCATE: message truncated
[t12node082:28692] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
--
mpiexec has exited due to process rank 31 with PID 28692 on
node t12node082 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--
[t12node084:17231] 8 more processes have sent help message
help-mpi-errors.txt / mpi_errors_are_fatal

Is my input in some way wrong, it's a problem of compilation of the code or
it is a bug? My code is compiled with gcc/gfortran and OpenMPI.
I'm reporting my input for reference below.
Thanks lot in advance and best regards,
Mauro Sgroi.
Centro Ricerche FIAT, Italy.

BEGIN
BEGIN_PATH_INPUT

  restart_mode  = 'from_scratch'
  string_method = 'neb',
  nstep_path= 200,
  ds= 1.D0,
  opt_scheme= "broyden2",
  num_of_images = 7,
  k_max = 0.3D0,
  k_min = 0.2D0,
  CI_scheme = "auto",
  path_thr  = 0.1D0,
  first_last_opt= .true.
/
END_PATH_INPUT

BEGIN_ENGINE_INPUT

pseudo_dir='/data5/sgroi/DATABASE/ESPRESSO',
prefix='mnpo4_121_gamma',
outdir='/net/manager/remote/qespresso/mnpo4_121_gamma',
wf_collect=.false.,
disk_io='none',
/


ibrav=8,
nat=49,
ntyp=5,
ecutwfc=78,
ecutrho=355,
nbnd=240,
occupations='smearing',
degauss=1d-10,
smearing='mv',
nspin=2,
starting_magnetization(1)=0.9,
starting_magnetization(2)=0.9,
lda_plus_u=.true.,
Hubbard_U(1)= 4.5,
Hubbard_U(2)=5.695,
celldm(1)=18.49395,
celldm(2)=1.21346602537586616163,
celldm(3)=0.49381770795314143273
/


conv_thr=1.0d-9,
electron_maxstep=200,
mixing_beta=0.5,
scf_must_converge=.false.
/

ATOMIC_SPECIES
 Mn 54.9381 Mn.pbesol-spn-kjpaw_psl.0.3.1.UPF
 Co 58.933195 Co.pbesol-n-kjpaw_psl.0.2.3.UPF
 P 30.9737  P.pbesol-n-kjpaw_psl.0.1.UPF
 O 15.9994  O.pbesol-n-kjpaw_psl.0.1.UPF
 Li 6.941   Li.pbesol-s-kjpaw_psl.0.2.1.UPF

BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { crystal }
Li0.5   0.25  0.5
Co0.290725910.12500.91347261
Co0.290725910.62500.91347261
Mn0.709274090.87500.08652739
Mn0.709274090.37500.08652739
Mn0.209274090.87500.41347261
Mn0.209274090.37500.41347261
Mn0.790725910.12500.58652739
Mn0.790725910.62500.58652739
P0.100843650.12500.40451768
P0.100843650.62500.40451768
P0.899156350.87500.59548232
P0.899156350.37500.59548232
P0.399156350.87500.90451768
P0.399156350.37500.90451768
P0.600843650.12500.09548232
P0.600843650.62500.09548232
O0.123851740.12500.71580776
O0.123851740.62500.71580776
O0.876148260.87500.28419224
O0.876148260.37500.28419224
O0.376148250.87500.21580776
O0.376148250.37500.21580776
O0.623851740.12500.78419224
O0.623851740.62500.78419224
O0.446242230.12500.14543042
O0.446242230.62500.14543042
O0.553757770.87500.85456959
O0.553757770.37500.85456959
O0.053757770.87500.64543041
O0.053757770.37500.64543041
O0.946242230.12500.35456959
O0.946242230.62500.35456959
O0.829949470.474731250.74215029
O0.829949470.974731250.74215029
O  

[Pw_forum] AiiDA released - a new platform for materials' informatics

[Giovanni Pizzi]

Dear Quantum ESPRESSO users,

we are happy to announce that AiiDA - a materials' informatics Python
platform to manage, store, organize, query and share large amounts of
data, calculations, and workflows - has been recently released and can
be freely downloaded from the website http://www.aiida.net.

A preprint describing AiiDA is available on arXiv at
http://arxiv.org/abs/1504.01163 while extensive code documentation for
users and developers (installation instructions, tutorials, user and
development manuals) is distributed with the code and available
online at

 http://aiida-core.readthedocs.org/en/stable/

The core of the software ("aiida_core") is released under an open-source
MIT license and can be freely downloaded (no registration necessary) from
the AiiDA website or from BitBucket:

 http://www.aiida.net/?page_id=264
 https://bitbucket.org/aiida_team/aiida_core

"aiida_core" is complemented by an extended set of plugins; these are
free and distributed with the code provided you belong to an
academic institution. These plugins provide support for various
simulation packages, including the Quantum ESPRESSO codes pw.x, cp.x,
ph.x, matdyn.x, q2r.x.
This extended version ("aiida_epfl", that includes "aiida_core")
can be obtained from

 http://theossrv1.epfl.ch/aiida_download/

Hoping that you may find AiiDA useful for your research,

Giovanni Pizzi on behalf of the AiiDA team
(http://www.aiida.net/?page_id=34)


-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (Bâtiment MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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[Pw_forum] cif to pwi

[Winfred Mulwa]

Dear all,
please somebody help me get a supercell of  100 atoms in  pwi  format
from the attached  cif   file.
Kind regards
Mulwa Winfred.
D Phil Student, Computational Material Science Group,
University of the Free State - QwaQwa,
South Africa.


win3.cif
Description: application/vnd.multiad.creator.cif
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Re: [Pw_forum] Pw_forum Digest, Vol 95, Issue 14

[Yusuf Zuntu]

Re: Pw_forum Digest, Vol 95, Issue 11 ( total magnetization and absolute 
magnetization quenched)

Dear Prof Paolo,

Thank you for your swift response. Although I do not completely capture your 
response " they use different pseudopotentials and k-points" but am optimistic 
to learn more as to the reason for this strange change. In my relax 
calculation, the magnetic moment agrees well with the reported values and using 
QE pseudopotential with lesser number of k-points mesh, unfortunately, magnetic 
moment completely quenched in scf calculation and using the same QE 
pseudopotential at high k-points mesh. I will be happy to know the reason for 
the change with regards to their pseudo 
"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.108.197207; (check 
here in) and what to modify to be able to repeat the same calculations: find 
below the input files for relax and scf calculations used
RELAX CALCULATION


calculation = 'relax' ,
  title  = 'C4N3'
prefix='pbe1x1C4N3',
 restart_mode = 'from_scratch' ,
 outdir = '/home/zuntu/yusuf/espresso-5.1.1/bin'
pseudo_dir='/home/zuntu/yusuf/espresso-5.1.1/pseudo/upf_files'
tstress = .true. ,
tprnfor = .true. ,

 /

ibrav=4, celldm(1)= 9.14623, celldm(3)= 3.22190083 
nat= 7, ntyp= 2,
ecutwfc =40.0, ecutrho = 270, tot_charge = 0.00,
 occupations = 'smearing' ,
 degauss = 0.01 ,
 smearing = 'mp' ,
  nspin = 2 ,
   starting_magnetization(1) = 0.3,
 /
 
conv_thr = 1.D-6 ,
 mixing_beta = 0.7D0 ,
/
 
ion_dynamics = 'bfgs' ,
   pot_extrapolation = 'second_order' ,
   wfc_extrapolation = 'second_order' ,
 /
ATOMIC_SPECIES
 C  12.0107 C.pbe-n-kjpaw_psl.0.1.UPF
 N  14.0067 N.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS angstrom
 C 0.0 0.0 2.0
 C 1.21 0.64 2.  
 N 2.42 0.00 2.00  
 C 3.63 0.674 2.0  
 N 3.63 2.022 2.  
 C 2.42 2.68 2.00
 N 1.21 2.022 2.0
K_POINTS automatic
   4 4 1 1 1 1

SCF CALCULATION


calculation = 'scf' ,
  title  = 'C4N3'
prefix='pbe1x1C4N3',
 restart_mode = 'from_scratch' ,
 outdir = '/home/zuntu/yusuf/espresso-5.1.1/bin'
pseudo_dir='/home/zuntu/yusuf/espresso-5.1.1/pseudo/upf_files'
 verbosity='high'

 /

ibrav=4, celldm(1)= 9.14623, celldm(3)= 3.22190083 
nat= 7, ntyp= 2,
ecutwfc =40.0, ecutrho = 270, tot_charge = 0.00,
 occupations = 'smearing' ,
 degauss = 0.01 ,
 smearing = 'mp' ,
 nspin = 2 ,
   starting_magnetization(1) = 0.6,
 /
 
conv_thr = 1.D-6 ,
 mixing_beta = 0.7D0 ,
/
ATOMIC_SPECIES
 C  12.0107 C.pz-n-kjpaw_psl.0.1.UPF
 N  14.0067 N.pz-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS (angstrom)
C0.000169362  -0.049027525   2.01268
C1.246828369   0.669477960   2.01487
N2.420687939   0.008258827   1.96634
C3.593997961   0.670979132   2.02839
N3.579281825   2.018019377   1.98410
C2.419168269   2.703396539   2.03594
N1.259866274   2.016895690   1.95769
K_POINTS automatic
 12 12 1 1 1 1 
  
Thank you

Yusuf Zuntu
Postgraduate Student
Universiti Sains Malaysia
---e
On Mon, 6/15/15, pw_forum-requ...@pwscf.org  wrote:

 Subject: Pw_forum Digest, Vol 95, Issue 14
 To: pw_forum@pwscf.org
 Date: Monday, June 15, 2015, 6:00 PM
 
 Send Pw_forum mailing list
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     pw_forum@pwscf.org
 
 To subscribe or unsubscribe via the World Wide Web, visit
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 or, via email, send a message with subject or body 'help'
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 When replying, please edit your Subject line so it is more
 specific
 than "Re: Contents of Pw_forum digest..."
 
 
 Today's Topics:
 
    1. Re: [*]  Re:  [qe-gpu]
 (Anubhav Kumar)
    2. Re: Pw_forum Digest, Vol 95, Issue 13
 (Umesh Roy)
    3. Re: Bug (or not) with epsil = .false.
 in PH (trunk version)
       (Andrea Dal Corso)
    4. Re: Pw_forum Digest, Vol 95, Issue 11
 (Yusuf Zuntu)
    5. Re: Pw_forum Digest, Vol 95, Issue 11
 (Paolo Giannozzi)
 
 
 --
 
 Message: 1
 Date: Sun, 14 Jun 2015 15:57:41 +0530
 From: "Anubhav Kumar" 
 Subject: Re: [Pw_forum] [*]  Re:  [qe-gpu]
 To: "PWSCF Forum" 
 Message-ID:
     <2447241701e01ab85061153de3e2d335.squir...@webmail.iitk.ac.in>
 Content-Type: text/plain;charset=iso-8859-1
 
 Dear Filippo
 
 Thank you very much for your reply.I am new to parallel
 programming and
 cuda.So can you please explain in detail how to make changes
 suggested by
 you?
 
 > Dear Anubhav,
 >
 > run in parallel, 2 MPI and make sure
 CUDA_VISIBLE_DEVICES is set such
 >
 > MPI rank 0 -> GPU id 1 (K20)
 > MPI rank 1 -> GPU id 2 (K20)
 >
 > Those K20 GPU are active cooled cards, how many 

[Pw_forum] Raman Spectra

[Amreen Bano]

Respected Sir/Mam,
I am working on optical properties.
I have run dynmat.x file and obtained the output below:

# mode   [cm-1][THz]  IR  Raman   depol.fact
1   -487.60  -14.6178   37.7287   277.86090.6461
2 -0.00   -0.0.334597.41700.7437
3 -0.00   -0.0.  8113.29750.7291
4 -0.00   -0.0. 25779.90200.7455
5  0.000.0.  6417.84420.6634
6  0.000.0.   171.70540.6246
7  0.000.0. 29050.28080.7489
8 56.801.70284.4068273118.78750.7446
9160.494.8115   11.3630 55305.28850.7395
   10223.346.69543.8373 91527.11270.7438
   11327.829.82772.9918 21597.63730.7373
   12351.66   10.54241.9769   1081889.82250.7431
   13555.84   16.66373.8963 13013.88340.2450
   14748.23   22.43159.1009  3164.22750.1576
   15790.74   23.70595.1725   764.08950.5078.
With the 2nd and 5th column i can form raman spectra, but output contains
very few values which is giving abnormal plot.
how can i plot a correct and smooth plot for raman spectra.
please suggest me the correct path.

-- 
Amreen Bano
Department of Physics,
Barkatullah University,
Bhopal-462 026
INDIA
+91-9993515955
banoamree...@gmail.com
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[Pw_forum] Projection of dos on to molecular orbitals

[vasudevan m.v]

Dear QE users,

I want to project the density of states of complete system (molecule
adsorbed on a surface) on to molecular orbitals of adsorbate and find
population of different molecular orbitals. If I understood correctly there
is an post-processing tool molecularpdos.x in quantum ESPRESSO v 5.1.2
which does this job. If I am mistaken please correct me. (
http://www.quantum-espresso.org/wp-content/uploads/Doc/pp_user_guide/node8.html
)

Statement 1)

>From /espresso-5.1.2/PP/Doc/INPUT_molecularpdos.html

 " *Then the eigenvectors of the full system are projected onto the ones of
the part. For example, to decompose the PDOS of an adsorbed molecule into
its molecular orbital, as determined by a gas-phase calculation*"

I don't understand what is meant by decomposition of pdos while in first
part it says eigenvectors of full system are used.

Statement 2)

"*The atomic wavefunctions identified by the ranges
 i_atmwfc_beg_full:i_atmwfc_end_full (full system) and
 i_atmwfc_beg_part:i_atmwfc_end_part (molecular part)  should correspond to
the same atomic states. See the  header of the output of projwfc.x for more
information*."

I feel the above statement slightly confusing as in statement 1 it is said
that "*Then the eigenvectors of the full system are projected onto the ones
of the part*"

Hope that things are conveyed well.

With regards
Vasudevan M V
JNCASR
Bangalore
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Re: [Pw_forum] Pw_forum Digest, Vol 95, Issue 11

[Paolo Giannozzi]

On Mon, Jun 15, 2015 at 10:56 AM, Yusuf Zuntu  wrote:

Input files for relax and scf attached.
>

they use different pseudopotentials and k-points

P.
-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
hone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] Pw_forum Digest, Vol 95, Issue 11

[Yusuf Zuntu]

Topic:
total magnetization and absolute
magnetization quenched.

Dear Quantum Espresso users,

Can some one bail me out of this problem. In trying to repeat some calculations 
of this article 
"http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.108.197207;, an 
unexpected magnetic behavior manifest between relax and scf calculations. Below 
are the details of the output:

Relax calculation

 the Fermi energy is-3.1983 ev

!total energy  =-158.20644301 Ry
 Harris-Foulkes estimate   =-158.20644301 Ry
 estimated scf accuracy<  3.5E-09 Ry

 total all-electron energy =  -633.159253 Ry

 The total energy is the sum of the following terms:

 one-electron contribution =-664.83395884 Ry
 hartree contribution  = 338.58658021 Ry
 xc contribution   = -32.69935803 Ry
 ewald contribution= 252.19023776 Ry
 one-center paw contrib.   = -51.45032393 Ry
 smearing contrib. (-TS)   =   0.00037981 Ry

 total magnetization   = 1.00 Bohr mag/cell
 absolute magnetization= 1.08 Bohr mag/cell

 convergence has been achieved in   5 iterations

 Forces acting on atoms (Ry/au):


 negative rho (up, down):  3.821E-04 3.015E-04
 atom1 type  1   force =-0.00036461   -0.000342330.0075
 atom2 type  1   force =-0.000629030.000154880.0019
 atom3 type  2   force =-0.000134860.00026628   -0.0034
 atom4 type  1   force = 0.00046437   -0.00072125   -0.0023
 atom5 type  2   force = 0.00015269   -0.4785   -0.0012
 atom6 type  1   force = 0.000255660.00039710   -0.0008
 atom7 type  2   force = 0.000255780.00029316   -0.0017

 Total force = 0.001377 Total SCF correction = 0.000117


 entering subroutine stress ...


 negative rho (up, down):  3.821E-04 3.015E-04
  total   stress  (Ry/bohr**3)   (kbar) P=   -1.16
  -0.1005   0.0007  -0. -1.48  0.01 -0.00
   0.0007  -0.1037   0.  0.01 -1.53  0.00
  -0.   0.  -0.0322 -0.00  0.00 -0.47


 bfgs converged in   7 scf cycles and   6 bfgs steps
 (criteria: energy <  1.0E-04, force <  1.0E-03)

 End of BFGS Geometry Optimization

 Final energy   =-158.2064430134 Ry
Begin final coordinates

ATOMIC_POSITIONS (angstrom)
C0.000169362  -0.049027525   2.01268
C1.246828369   0.669477960   2.01487
N2.420687939   0.008258827   1.96634
C3.593997961   0.670979132   2.02839
N3.579281825   2.018019377   1.98410
C2.419168269   2.703396539   2.03594
N1.259866274   2.016895690   1.95769
End final coordinates.

SCF calculation:

the Fermi energy is-3.3467 ev

!total energy  =-110.83170176 Ry
 Harris-Foulkes estimate   =-110.83170172 Ry
 estimated scf accuracy<   0.0008 Ry

 The total energy is the sum of the following terms:

 one-electron contribution =-665.86218544 Ry
 hartree contribution  = 338.49928445 Ry
 xc contribution   = -35.54208467 Ry
 ewald contribution= 252.07341919 Ry
 smearing contrib. (-TS)   =  -0.00013530 Ry

 total magnetization   =-0.00 Bohr mag/cell
 absolute magnetization= 0.00 Bohr mag/cell

 convergence has been achieved in  14 iterations.

Input files for relax and scf attached.

Yusuf Zuntu

Postgraduate Student
Universiti Sains Malaysia 

On Fri, 6/12/15, pw_forum-requ...@pwscf.org  wrote:

 Subject: Pw_forum Digest, Vol 95, Issue 11
 To: pw_forum@pwscf.org
 Date: Friday, June 12, 2015, 6:00 PM
 
 Send Pw_forum mailing list
 submissions to
     pw_forum@pwscf.org
 
 To subscribe or unsubscribe via the World Wide Web, visit
     http://pwscf.org/mailman/listinfo/pw_forum
 or, via email, send a message with subject or body 'help'
 to
     pw_forum-requ...@pwscf.org
 
 You can reach the person managing the list at
     pw_forum-ow...@pwscf.org
 
 When replying, please edit your Subject line so it is more
 specific
 than "Re: Contents of Pw_forum digest..."
 
 
 Today's Topics:
 
    1. Re: total magnetization and absolute
 magnetization (Elham)
    2. Re: total magnetization and absolute
 magnetization
       (Arles V. Gil Rebaza)
    3. looking for optimal k-point sampling
 specific to    monoclinic
       cells (Manuel P?rez Jigato)
    4. spin polarization (Tayebeh Roohande)
    5. Re: PLUMED and Quantum-ESPRESSO (Paolo
 Giannozzi)
    6. Re: spin polarization (Mostafa
 Youssef)
 
 
 --
 
 Message: 1
 Date: Thu, 11 Jun 2015 14:49:51 +0430
 From: Elham 

Re: [Pw_forum] Bug (or not) with epsil = .false. in PH (trunk version)

[Andrea Dal Corso]

On Sat, 2015-06-13 at 16:38 +0100, Samuel Poncé wrote:
> Dear all,
> 
> I found out that it was impossible de make a phonon calculation without
> calculating the Born effective charge in a semi-conductor even if we set
> epsil = .false.
> 
> This is due to the routine prepare_q.f90 that is called inside do_phonon.f90
> In the routine there is
>  IF ( lgamma ) THEN
> !
> IF ( .NOT. lgauss ) THEN
>!
>! ... in the case of an insulator at q=0 one has to calculate
>! ... the dielectric constant and the Born eff. charges
>! ... the other flags depend on input
>!
>epsil = .TRUE.
>zeu = .TRUE.
>zue = .TRUE.
> 
> 
> This means that if we compute q=Gamma and if we do not have
> gaussian-smearing (i.e. an semi-cond or insulator), then epsil is
> automatically set to TRUE.
> 
> I know that physically one should have such LO/TO splitting but the user
> should be able to choose.
> 
> Maybe this forcing could be reported in the input variable ? or simply put
> the default value to .TRUE. instead of false and not enforcing that rule?
> 
> What do you think?

This is true only when ldisp=.TRUE.. If you do a phonon calculation at
gamma with ldisp=.FALSE. you can set/unset the dielectric constant
calculation with the flag epsil.

It has to be like this, otherwise the dispersion would show a jump at
gamma and the interpolation would not work.

HTH,

Andrea


> 
> Best,
> 
> Samuel Ponce,
> Department of Materials, University of Oxford
> ___
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-- 
Andrea Dal CorsoTel. 0039-040-3787428
SISSA, Via Bonomea 265  Fax. 0039-040-3787249
I-34136 Trieste (Italy) e-mail: dalco...@sissa.it


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